preproc QC missing image

Hi AFNI Gurus,

I was wondering if the image “qc_08_mot_grayplot.jpg” can be easily generated. When viewing the QC html file this particular file is empty and is missing from the html layout.

Thanks in advance,

-Ben

Hi, Ben-

In the ‘results’ directory from afni_proc.py processing, there should be a file called: out.review_html. It contains all the terminal output of executing the script @ss_review_html (same directory), which creates the QC images+content that gets put into the HTML.

Could you please email me both out.review_html and @ss_review_html for that subject? (They are a little long to post here, probably.)

thanks,
pt

*+ Found main dset (template): /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./vr_base_min_outlier+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./vr_base_min_outlier+orig.BRIK is 1.899913 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./vr_base_min_outlier+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./vr_base_min_outlier+orig.BRIK is 1.899913 degrees from plumb.
++ pbar name has known extension: jpg
++ My command:
@chauffeur_afni -ulay vr_base_min_outlier+orig.HEAD -olay vr_base_min_outlier+orig.HEAD -ulay_range_nz 0 362.947296 -func_range 362.947296 -box_focus_slices AMASK_FOCUS_ULAY -cbar gray_scale -pbar_posonly -pbar_saveim QC_sub-11481002_ses-1/media/qc_00_vorig_EPI.pbar.jpg -pbar_comm_range 98%ile in vol -pbar_for dset -prefix QC_sub-11481002_ses-1/media/qc_00_vorig_EPI -save_ftype JPEG -blowup 4 -opacity 9 -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean

++ Using AFNI ver : AFNI_21.2.04
++ chauffeur ver : 6.26

------------------ start of optionizing ------------------

++ Found input file: vr_base_min_outlier+orig.HEAD
++ Found input file: vr_base_min_outlier+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_sub-11481002_ses-1/media/__tmp_chauf_oQlvHggJyVi
++ Converted 0 to labels
++ Final subbrick indices: -1 -1 -1
++ Copy ulay to visualize (volumetric) within user’s range:
++ Ulay to be visualized within user range:
[0, 362.947296]
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__tmp_chauf_oQlvHggJyVi/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__tmp_chauf_oQlvHggJyVi/tmp_olay.nii
++ User-entered function range value value (362.947296)
++ Dimensions (xyzt): 90 90 60 1
++ (initial) Slice spacing ordered (x,y,z) is: 12 12 8
++ 3dAutomask: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Emperor Zhark
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./vr_base_min_outlier+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./vr_base_min_outlier+orig.BRIK is 1.899913 degrees from plumb.
++ 3dAutobox: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as /gpfs/data/sfeldste/ImagingData/Study/MINA/MINA_BIDS/sub-11481002/ses-1/derivatives/REST/sub-11481002_ses-1.results/QC_sub-11481002_ses-1/media/__tmp_chauf_oQlvHggJyVi/AMASK_FOCUS_ULAY.nii,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:/gpfs/data/sfeldste/ImagingData/Study/MINA/MINA_BIDS/sub-11481002/ses-1/derivatives/REST/sub-11481002_ses-1.results/QC_sub-11481002_ses-1/media/__tmp_chauf_oQlvHggJyVi/AMASK_FOCUS_ULAY.nii is 1.899913 degrees from plumb.
++ Auto bbox: x=15…74 y=6…89 z=0…58
++ 3dAutobox: output dataset = QC_sub-11481002_ses-1/media/__tmp_chauf_oQlvHggJyVi/ulay_box_0.nii
++ 3dmaskdump: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=QC_sub-11481002_ses-1/media/__tmp_chauf_oQlvHggJyVi/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_XYZ_L_wppdDyazz5Y7VAh7nMkA argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0: no scale factor
++ Computing output statistics
++ Output dataset /tmp/3dcalc_XYZ_L_wppdDyazz5Y7VAh7nMkA+orig.BRIK
++ 297360 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ How many coors? 3
++ Will have the ref box central coors : SET_DICOM_XYZ 4.532303 -19.40736 0.907936
++ Will have the ref box central gapord: 8 12 8

------------------- end of optionizing -------------------

– trying to start Xvfb :502
[1] 16198
+/gpfs/data/sfeldste/ImagingData/Study/MINA/MINA_BIDS/sub-11481002/ses-1/derivatives/REST/sub-11481002_ses-1.results/QC_sub-11481002_ses-1/media/__tmp_chauf_oQlvHggJyVi++ Writing palette image to QC_sub-11481002_ses-1/media/qc_00_vorig_EPI.pbar.jpg
++ Writing one 2544x240 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_00_vorig_EPI.sag.jpg’
++ Writing one 2544x240 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_00_vorig_EPI.cor.jpg’
++ Writing one 2544x360 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_00_vorig_EPI.axi.jpg’

AFNI QUITTs!

+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=7x1:8:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=7x1:12:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=7x1:8:1:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 gray_scale -com PBAR_SAVEIM QC_sub-11481002_ses-1/media/qc_00_vorig_EPI.pbar.jpg dim=64x512H -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0 362.947296 -com SET_FUNC_RANGE 362.947296 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 4.532303 -19.40736 0.907936 -com SAVE_JPEG sagittalimage QC_sub-11481002_ses-1/media/qc_00_vorig_EPI.sag blowup=4 -com SAVE_JPEG coronalimage QC_sub-11481002_ses-1/media/qc_00_vorig_EPI.cor blowup=4 -com SAVE_JPEG axialimage QC_sub-11481002_ses-1/media/qc_00_vorig_EPI.axi blowup=4 -com QUITT QC_sub-11481002_ses-1/media/__tmp_chauf_oQlvHggJyVi

+* Removing temporary image directory ‘QC_sub-11481002_ses-1/media/__tmp_chauf_oQlvHggJyVi’.

[1] + Done Xvfb :502 -screen 0 1024x768x24

++ DONE (good exit)
see: QC_sub-11481002_ses-1/media/qc_00_vorig_EPI*

++ Prepare for running @djunct_edgy_align_check (ver = 1.45)
++ Copy refbox (/gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz) to workdir
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__workdir_EAC_RGyfFTwwZh5/REFBOX.nii
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__workdir_EAC_RGyfFTwwZh5/eac_0_cp.nii
++ 3dAllineate: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /gpfs/data/sfeldste/ImagingData/Study/MINA/MINA_BIDS/sub-11481002/ses-1/derivatives/REST/sub-11481002_ses-1.results/QC_sub-11481002_ses-1/media/__workdir_EAC_RGyfFTwwZh5/eac_0_cp.nii
++ Base dataset: (not given)
++ Loading datasets into memory

  •    -cmass x y z shifts =    0.000    0.000    0.000
    
  • shift search range is +/- = 60.990 72.546 60.990
    ++ OpenMP thread count = 2
    ++ ========== Applying transformation to 1 sub-bricks ==========
    ++ wsinc5 interpolation setup:
  • taper function = Min sidelobe 3 term
  • taper cut point = 0.000
  • window radius = 5 voxels
  • window shape = Cubical
  • The above can be altered via the AFNI_WSINC5_* environment variables.
  • (To avoid this message, ‘setenv AFNI_WSINC5_SILENT YES’.)
  • wsinc5 CUBE(5) mask has 1000 points
    ++ Output dataset QC_sub-11481002_ses-1/media/__workdir_EAC_RGyfFTwwZh5/eac_1_grid2olay.nii
    ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 14.7
    ++ ###########################################################
    ++ Output dataset ./eac_2_ulay_shrp.nii
    ++ Just copy olay, bc ulay will get regridded
    ++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
    ++ Authored by: A cast of thousands
    ++ Output dataset ./QC_sub-11481002_ses-1/media/__workdir_EAC_RGyfFTwwZh5/eac_3_cp.nii
    ++ 3dAutomask: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
    ++ Authored by: Emperor Zhark
    ++ Loading dataset eac_3_cp.nii
    ++ Forming automask
  • Fixed clip level = 424.799561
  • Used gradual clip level = 401.676544 … 436.132111
  • Number voxels above clip level = 1673868
  • Clustering voxels …
  • Largest cluster has 1673660 voxels
  • Clustering voxels …
  • Largest cluster has 1668034 voxels
  • Filled 32954 voxels in small holes; now have 1700988 voxels
  • Filled 134896 voxels in large holes; now have 1835884 voxels
  • Clustering voxels …
  • Largest cluster has 1835879 voxels
  • Clustering non-brain voxels …
  • Clustering voxels …
  • Largest cluster has 6691659 voxels
  • Mask now has 1838362 voxels
    ++ 1838362 voxels in the mask [out of 8530021: 21.55%]
    ++ first 25 x-planes are zero [from L]
    ++ last 24 x-planes are zero [from R]
    ++ first 25 y-planes are zero [from P]
    ++ last 22 y-planes are zero [from A]
    ++ first 6 z-planes are zero [from I]
    ++ last 32 z-planes are zero [from S]
    ++ Output dataset ./eac_4_mask.nii
    ++ CPU time = 0.000000 sec
    ++ 3dMedianFilter: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
    ++ Output dataset ./eac_5_mfilt.nii
    ++ 3dedge3: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
    ++ olay_alpha has known value: No

++ My command:
@chauffeur_afni -ulay eac_2_ulay_shrp.nii -box_focus_slices REFBOX.nii -olay eac_6_edgy.nii -ulay_range_nz 2% 98% -func_range_perc_nz 33 -cbar Reds_and_Blues_Inv -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -thr_olay 23.742212 -opacity 9 -prefix …/qc_01_ve2a_epi2anat -montx 7 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass

++ Using AFNI ver : AFNI_21.2.04
++ chauffeur ver : 6.26

------------------ start of optionizing ------------------

++ Found input file: eac_2_ulay_shrp.nii
++ Found input file: eac_6_edgy.nii
++ Found focus refbox file: REFBOX.nii
+* NB: focus box vol has >1 slice, so we select [0]th.
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: …/__tmp_chauf_Kuq2TzfAalt
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user’s range:
++ Ulay to be visualized within user range:
[2%, 98%] → [-0.000000, 374.692230]
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./…/__tmp_chauf_Kuq2TzfAalt/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./…/__tmp_chauf_Kuq2TzfAalt/tmp_olay.nii
++ For olay, the 33%ile value leads to
→ upper range value: 325.360992
++ Dimensions (xyzt): 193 229 193 1
++ (initial) Slice spacing ordered (x,y,z) is: 27 32 27
++ 3dAutobox: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Auto bbox: x=24…168 y=25…205 z=6…160
++ 3dAutobox: output dataset = …/__tmp_chauf_Kuq2TzfAalt/ulay_box_0.nii
++ 3dmaskdump: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=…/__tmp_chauf_Kuq2TzfAalt/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_XYZ__gEcFV6XgXhfluoM3ysLVQ argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /tmp/3dcalc_XYZ__gEcFV6XgXhfluoM3ysLVQ+tlrc.BRIK
++ 4067975 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ How many coors? 3
++ Will have the ref box central coors : SET_DICOM_XYZ 1 17 5
++ Will have the ref box central gapord: 20 25 22

------------------- end of optionizing -------------------

– trying to start Xvfb :720
[1] 16519
+/gpfs/data/sfeldste/ImagingData/Study/MINA/MINA_BIDS/sub-11481002/ses-1/derivatives/REST/sub-11481002_ses-1.results/QC_sub-11481002_ses-1/media/__tmp_chauf_Kuq2TzfAalt++ Writing one 3218x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > …/qc_01_ve2a_epi2anat.sag.jpg’
++ Writing one 2714x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > …/qc_01_ve2a_epi2anat.cor.jpg’
++ Writing one 2714x458 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > …/qc_01_ve2a_epi2anat.axi.jpg’

AFNI QUITTs!

+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=7x1:20:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=7x1:25:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=7x1:22:1:black crop=0:0,0:0 -com SET_PBAR_ALL -99 1 Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all -0.000000 374.692230 -com SET_FUNC_RANGE 325.360992 -com SET_THRESHNEW 23.742212 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 1 17 5 -com SAVE_JPEG sagittalimage …/qc_01_ve2a_epi2anat.sag blowup=2 -com SAVE_JPEG coronalimage …/qc_01_ve2a_epi2anat.cor blowup=2 -com SAVE_JPEG axialimage …/qc_01_ve2a_epi2anat.axi blowup=2 -com QUITT …/__tmp_chauf_Kuq2TzfAalt

+* Removing temporary image directory ‘…/__tmp_chauf_Kuq2TzfAalt’.

[1] + Done Xvfb :720 -screen 0 1024x768x24

++ DONE (good exit)
see: …/qc_01_ve2a_epi2anat*

+* Removing temporary workdir ‘QC_sub-11481002_ses-1/media/__workdir_EAC_RGyfFTwwZh5*’

++ DONE! Image output:
QC_sub-11481002_ses-1/media/qc_01_ve2a_epi2anat

++ Prepare for running @djunct_edgy_align_check (ver = 1.45)
++ Copy refbox (/gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz) to workdir
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__workdir_EAC_tqMsxegGiA5/REFBOX.nii
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__workdir_EAC_tqMsxegGiA5/eac_0_cp.nii
++ Output dataset ./eac_1_ulay_shrp.nii
++ 3dAllineate: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /gpfs/rt/7.2/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
++ Base dataset: (not given)
++ Loading datasets into memory
+ WARNING: -1D_apply ‘1D: 12@0’': 1 isn’t enough rows for source dataset – last row will repeat

  •    -cmass x y z shifts =   -0.008   -0.005    0.029
    
  • shift search range is +/- = 61.632 73.188 61.632
    ++ OpenMP thread count = 2
    ++ ========== Applying transformation to 5 sub-bricks ==========
    volume 0…1*+ WARNING: Re-using final row of -1D*_apply ‘1D: 12@0’’ for sub-brick #1
    …2*+ WARNING: Re-using final row of -1D*_apply ‘1D: 12@0’’ for sub-brick #2
    …3*+ WARNING: Re-using final row of -1D*_apply ‘1D: 12@0’’ for sub-brick #3
    …4
    + WARNING: Re-using final row of -1D_apply ‘1D: 12@0’’ for sub-brick #4
    ++ Output dataset QC_sub-11481002_ses-1/media/__workdir_EAC_tqMsxegGiA5/eac_2_res.nii
    ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 11.0
    ++ ###########################################################
    ++ 3dAutomask: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
    ++ Authored by: Emperor Zhark
    ++ Loading dataset eac_2_res.nii
    ++ Forming automask
  • Fixed clip level = 866.280640
  • Used gradual clip level = 839.463562 … 889.332031
  • Number voxels above clip level = 1839751
  • Clustering voxels …
  • Largest cluster has 1839749 voxels
  • Clustering voxels …
  • Largest cluster has 1839644 voxels
  • Filled 2255 voxels in small holes; now have 1841899 voxels
  • Filled 40056 voxels in large holes; now have 1881955 voxels
  • Clustering voxels …
  • Largest cluster has 1881949 voxels
  • Clustering non-brain voxels …
  • Clustering voxels …
  • Largest cluster has 6644410 voxels
  • Mask now has 1885611 voxels
    ++ 1885611 voxels in the mask [out of 8530021: 22.11%]
    ++ first 24 x-planes are zero [from L]
    ++ last 24 x-planes are zero [from R]
    ++ first 24 y-planes are zero [from P]
    ++ last 23 y-planes are zero [from A]
    ++ first 6 z-planes are zero [from I]
    ++ last 32 z-planes are zero [from S]
    ++ Output dataset ./eac_3_mask.nii
    ++ CPU time = 0.000000 sec
    ++ 3dMedianFilter: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
    *+ WARNING: Only processing sub-brick #0
    ++ Output dataset ./eac_4_mfilt.nii
    ++ 3dedge3: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
    ++ olay_alpha has known value: No

++ My command:
@chauffeur_afni -ulay eac_1_ulay_shrp.nii -box_focus_slices REFBOX.nii -olay eac_5_edgy.nii -ulay_range 0% 120% -func_range_perc_nz 33 -cbar Reds_and_Blues_Inv -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -thr_olay 22.371048 -opacity 9 -prefix …/qc_02_va2t_anat2temp -montx 7 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass

++ Using AFNI ver : AFNI_21.2.04
++ chauffeur ver : 6.26

------------------ start of optionizing ------------------

++ Found input file: eac_1_ulay_shrp.nii
++ Found input file: eac_5_edgy.nii
++ Found focus refbox file: REFBOX.nii
+* NB: focus box vol has >1 slice, so we select [0]th.
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: …/__tmp_chauf_Yl4EHgrUOkE
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user’s range:
++ Ulay range calc for >100%ile ulay max:
calculating 98%ile value, and then
multiplying it by a scale factor = 1.22448,
in order to produce the 98%ile value
++ Ulay to be visualized within user range:
[0%, 120%] → [0.000000, 1355.302504]
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./…/__tmp_chauf_Yl4EHgrUOkE/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./…/__tmp_chauf_Yl4EHgrUOkE/tmp_olay.nii
++ For olay, the 33%ile value leads to
→ upper range value: 344.516327
++ Dimensions (xyzt): 193 229 193 1
++ (initial) Slice spacing ordered (x,y,z) is: 27 32 27
++ 3dAutobox: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Auto bbox: x=24…168 y=25…205 z=6…160
++ 3dAutobox: output dataset = …/__tmp_chauf_Yl4EHgrUOkE/ulay_box_0.nii
++ 3dmaskdump: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=…/__tmp_chauf_Yl4EHgrUOkE/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_XYZ_JsHQ6NnwoSOpW6NbTZJKfA argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /tmp/3dcalc_XYZ_JsHQ6NnwoSOpW6NbTZJKfA+tlrc.BRIK
++ 4067975 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ How many coors? 3
++ Will have the ref box central coors : SET_DICOM_XYZ 1 17 5
++ Will have the ref box central gapord: 20 25 22

------------------- end of optionizing -------------------

– trying to start Xvfb :345
[1] 16837
+/gpfs/data/sfeldste/ImagingData/Study/MINA/MINA_BIDS/sub-11481002/ses-1/derivatives/REST/sub-11481002_ses-1.results/QC_sub-11481002_ses-1/media/__tmp_chauf_Yl4EHgrUOkE++ Writing one 3218x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > …/qc_02_va2t_anat2temp.sag.jpg’
++ Writing one 2714x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > …/qc_02_va2t_anat2temp.cor.jpg’
++ Writing one 2714x458 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > …/qc_02_va2t_anat2temp.axi.jpg’

AFNI QUITTs!

+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=7x1:20:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=7x1:25:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=7x1:22:1:black crop=0:0,0:0 -com SET_PBAR_ALL -99 1 Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1355.302504 -com SET_FUNC_RANGE 344.516327 -com SET_THRESHNEW 22.371048 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 1 17 5 -com SAVE_JPEG sagittalimage …/qc_02_va2t_anat2temp.sag blowup=2 -com SAVE_JPEG coronalimage …/qc_02_va2t_anat2temp.cor blowup=2 -com SAVE_JPEG axialimage …/qc_02_va2t_anat2temp.axi blowup=2 -com QUITT …/__tmp_chauf_Yl4EHgrUOkE

+* Removing temporary image directory ‘…/__tmp_chauf_Yl4EHgrUOkE’.

[1] + Done Xvfb :345 -screen 0 1024x768x24

++ DONE (good exit)
see: …/qc_02_va2t_anat2temp*

+* Removing temporary workdir ‘QC_sub-11481002_ses-1/media/__workdir_EAC_tqMsxegGiA5*’

++ DONE! Image output:
QC_sub-11481002_ses-1/media/qc_02_va2t_anat2temp

++ 3dmaskave: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
+++ 1050624 voxels in the entire dataset (no mask)
++ 28 voxels in the boxes+balls
++ 28 voxels in the mask INTERSECT boxes+balls
++ 3dTcorr1D: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]

  • reading dataset file errts.sub-11481002_ses-1.anaticor+tlrc.HEAD
  • reading 1D file _tmp_ave_ts.txt
  • loading dataset ./errts.sub-11481002_ses-1.anaticor+tlrc.BRIK into memory
    ++ Start correlations: 1050624 voxels X 1 time series(754); 1 threads
    *+ WARNING: THD_Tcorr1D: 168796 voxels skipped because were constant in time
    ++ Wrote dataset: ./_tmp_corr_vol.nii
    ++ olay_alpha has known value: Yes
    ++ pbar name has known extension: jpg
    ++ My command:
    @chauffeur_afni -ulay /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz -box_focus_slices /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz -olay _tmp_corr_vol.nii -cbar Reds_and_Blues_Inv -ulay_range 0% 120% -func_range 0.6 -thr_olay 0.3 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_sub-11481002_ses-1/media/qc_03_vstat_seed_lh-PCC.pbar.jpg -pbar_comm_range Pearson r -pbar_comm_thr alpha+boxed on -prefix QC_sub-11481002_ses-1/media/qc_03_vstat_seed_lh-PCC -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean

++ Using AFNI ver : AFNI_21.2.04
++ chauffeur ver : 6.26

------------------ start of optionizing ------------------

++ Found input file: /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
++ Found input file: _tmp_corr_vol.nii
++ Found focus refbox file: /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
+* NB: focus box vol has >1 slice, so we select [0]th.
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_sub-11481002_ses-1/media/__tmp_chauf_9YlhYrzR3AU
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user’s range:
++ Ulay range calc for >100%ile ulay max:
calculating 98%ile value, and then
multiplying it by a scale factor = 1.22448,
in order to produce the 98%ile value
++ Ulay to be visualized within user range:
[0%, 120%] → [0.000000, 1296.724320]
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__tmp_chauf_9YlhYrzR3AU/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__tmp_chauf_9YlhYrzR3AU/tmp_olay.nii
++ User-entered function range value value (0.6)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 27 32 27
++ 3dAutobox: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Auto bbox: x=24…168 y=25…205 z=6…160
++ 3dAutobox: output dataset = QC_sub-11481002_ses-1/media/__tmp_chauf_9YlhYrzR3AU/ulay_box_0.nii
++ 3dmaskdump: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=QC_sub-11481002_ses-1/media/__tmp_chauf_9YlhYrzR3AU/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_XYZ_2ajGLX9GjX-yd27whPV0rA argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /tmp/3dcalc_XYZ_2ajGLX9GjX-yd27whPV0rA+tlrc.BRIK
++ 4067975 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ How many coors? 3
++ Will have the ref box central coors : SET_DICOM_XYZ 1 17 5
++ Will have the ref box central gapord: 20 25 22

------------------- end of optionizing -------------------

– trying to start Xvfb :627
[1] 17141
+/gpfs/data/sfeldste/ImagingData/Study/MINA/MINA_BIDS/sub-11481002/ses-1/derivatives/REST/sub-11481002_ses-1.results/QC_sub-11481002_ses-1/media/__tmp_chauf_9YlhYrzR3AU++ Writing palette image to QC_sub-11481002_ses-1/media/qc_03_vstat_seed_lh-PCC.pbar.jpg
++ Writing one 3218x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_03_vstat_seed_lh-PCC.sag.jpg’
++ Writing one 2714x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_03_vstat_seed_lh-PCC.cor.jpg’
++ Writing one 2714x458 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_03_vstat_seed_lh-PCC.axi.jpg’

AFNI QUITTs!

+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=7x1:20:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=7x1:25:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=7x1:22:1:black crop=0:0,0:0 -com SET_PBAR_ALL -99 1 Reds_and_Blues_Inv -com PBAR_SAVEIM QC_sub-11481002_ses-1/media/qc_03_vstat_seed_lh-PCC.pbar.jpg dim=64x512H -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1296.724320 -com SET_FUNC_RANGE 0.6 -com SET_THRESHNEW 0.3 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 1 17 5 -com SAVE_JPEG sagittalimage QC_sub-11481002_ses-1/media/qc_03_vstat_seed_lh-PCC.sag blowup=2 -com SAVE_JPEG coronalimage QC_sub-11481002_ses-1/media/qc_03_vstat_seed_lh-PCC.cor blowup=2 -com SAVE_JPEG axialimage QC_sub-11481002_ses-1/media/qc_03_vstat_seed_lh-PCC.axi blowup=2 -com QUITT QC_sub-11481002_ses-1/media/__tmp_chauf_9YlhYrzR3AU

+* Removing temporary image directory ‘QC_sub-11481002_ses-1/media/__tmp_chauf_9YlhYrzR3AU’.

[1] + Done Xvfb :627 -screen 0 1024x768x24

++ DONE (good exit)
see: QC_sub-11481002_ses-1/media/qc_03_vstat_seed_lh-PCC*

++ 3dmaskave: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
+++ 1050624 voxels in the entire dataset (no mask)
++ 28 voxels in the boxes+balls
++ 28 voxels in the mask INTERSECT boxes+balls
++ 3dTcorr1D: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]

  • reading dataset file errts.sub-11481002_ses-1.anaticor+tlrc.HEAD
  • reading 1D file _tmp_ave_ts.txt
  • loading dataset ./errts.sub-11481002_ses-1.anaticor+tlrc.BRIK into memory
    ++ Start correlations: 1050624 voxels X 1 time series(754); 1 threads
    *+ WARNING: THD_Tcorr1D: 168796 voxels skipped because were constant in time
    ++ Wrote dataset: ./_tmp_corr_vol.nii
    ++ olay_alpha has known value: Yes
    ++ pbar name has known extension: jpg
    ++ My command:
    @chauffeur_afni -ulay /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz -box_focus_slices /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz -olay _tmp_corr_vol.nii -cbar Reds_and_Blues_Inv -ulay_range 0% 120% -func_range 0.6 -thr_olay 0.3 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_sub-11481002_ses-1/media/qc_04_vstat_seed_rh-cort-vis.pbar.jpg -pbar_comm_range Pearson r -pbar_comm_thr alpha+boxed on -prefix QC_sub-11481002_ses-1/media/qc_04_vstat_seed_rh-cort-vis -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean

++ Using AFNI ver : AFNI_21.2.04
++ chauffeur ver : 6.26

------------------ start of optionizing ------------------

++ Found input file: /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
++ Found input file: _tmp_corr_vol.nii
++ Found focus refbox file: /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
+* NB: focus box vol has >1 slice, so we select [0]th.
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_sub-11481002_ses-1/media/__tmp_chauf_AkrsMParkmD
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user’s range:
++ Ulay range calc for >100%ile ulay max:
calculating 98%ile value, and then
multiplying it by a scale factor = 1.22448,
in order to produce the 98%ile value
++ Ulay to be visualized within user range:
[0%, 120%] → [0.000000, 1296.724320]
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__tmp_chauf_AkrsMParkmD/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__tmp_chauf_AkrsMParkmD/tmp_olay.nii
++ User-entered function range value value (0.6)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 27 32 27
++ 3dAutobox: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Auto bbox: x=24…168 y=25…205 z=6…160
++ 3dAutobox: output dataset = QC_sub-11481002_ses-1/media/__tmp_chauf_AkrsMParkmD/ulay_box_0.nii
++ 3dmaskdump: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=QC_sub-11481002_ses-1/media/__tmp_chauf_AkrsMParkmD/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_XYZ_MAQsXvN1D8sk6u7CQPeiBQ argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /tmp/3dcalc_XYZ_MAQsXvN1D8sk6u7CQPeiBQ+tlrc.BRIK
++ 4067975 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ How many coors? 3
++ Will have the ref box central coors : SET_DICOM_XYZ 1 17 5
++ Will have the ref box central gapord: 20 25 22

------------------- end of optionizing -------------------

– trying to start Xvfb :314
[1] 17426
+/gpfs/data/sfeldste/ImagingData/Study/MINA/MINA_BIDS/sub-11481002/ses-1/derivatives/REST/sub-11481002_ses-1.results/QC_sub-11481002_ses-1/media/__tmp_chauf_AkrsMParkmD++ Writing palette image to QC_sub-11481002_ses-1/media/qc_04_vstat_seed_rh-cort-vis.pbar.jpg
++ Writing one 3218x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_04_vstat_seed_rh-cort-vis.sag.jpg’
++ Writing one 2714x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_04_vstat_seed_rh-cort-vis.cor.jpg’
++ Writing one 2714x458 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_04_vstat_seed_rh-cort-vis.axi.jpg’

AFNI QUITTs!

+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=7x1:20:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=7x1:25:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=7x1:22:1:black crop=0:0,0:0 -com SET_PBAR_ALL -99 1 Reds_and_Blues_Inv -com PBAR_SAVEIM QC_sub-11481002_ses-1/media/qc_04_vstat_seed_rh-cort-vis.pbar.jpg dim=64x512H -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1296.724320 -com SET_FUNC_RANGE 0.6 -com SET_THRESHNEW 0.3 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 1 17 5 -com SAVE_JPEG sagittalimage QC_sub-11481002_ses-1/media/qc_04_vstat_seed_rh-cort-vis.sag blowup=2 -com SAVE_JPEG coronalimage QC_sub-11481002_ses-1/media/qc_04_vstat_seed_rh-cort-vis.cor blowup=2 -com SAVE_JPEG axialimage QC_sub-11481002_ses-1/media/qc_04_vstat_seed_rh-cort-vis.axi blowup=2 -com QUITT QC_sub-11481002_ses-1/media/__tmp_chauf_AkrsMParkmD

+* Removing temporary image directory ‘QC_sub-11481002_ses-1/media/__tmp_chauf_AkrsMParkmD’.

[1] + Done Xvfb :314 -screen 0 1024x768x24

++ DONE (good exit)
see: QC_sub-11481002_ses-1/media/qc_04_vstat_seed_rh-cort-vis*

++ 3dmaskave: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
+++ 1050624 voxels in the entire dataset (no mask)
++ 32 voxels in the boxes+balls
++ 32 voxels in the mask INTERSECT boxes+balls
++ 3dTcorr1D: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]

  • reading dataset file errts.sub-11481002_ses-1.anaticor+tlrc.HEAD
  • reading 1D file _tmp_ave_ts.txt
  • loading dataset ./errts.sub-11481002_ses-1.anaticor+tlrc.BRIK into memory
    ++ Start correlations: 1050624 voxels X 1 time series(754); 1 threads
    *+ WARNING: THD_Tcorr1D: 168796 voxels skipped because were constant in time
    ++ Wrote dataset: ./_tmp_corr_vol.nii
    ++ olay_alpha has known value: Yes
    ++ pbar name has known extension: jpg
    ++ My command:
    @chauffeur_afni -ulay /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz -box_focus_slices /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz -olay _tmp_corr_vol.nii -cbar Reds_and_Blues_Inv -ulay_range 0% 120% -func_range 0.6 -thr_olay 0.3 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_sub-11481002_ses-1/media/qc_05_vstat_seed_lh-cort-aud.pbar.jpg -pbar_comm_range Pearson r -pbar_comm_thr alpha+boxed on -prefix QC_sub-11481002_ses-1/media/qc_05_vstat_seed_lh-cort-aud -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean

++ Using AFNI ver : AFNI_21.2.04
++ chauffeur ver : 6.26

------------------ start of optionizing ------------------

++ Found input file: /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
++ Found input file: _tmp_corr_vol.nii
++ Found focus refbox file: /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
+* NB: focus box vol has >1 slice, so we select [0]th.
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_sub-11481002_ses-1/media/__tmp_chauf_mUATxVdkin0
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user’s range:
++ Ulay range calc for >100%ile ulay max:
calculating 98%ile value, and then
multiplying it by a scale factor = 1.22448,
in order to produce the 98%ile value
++ Ulay to be visualized within user range:
[0%, 120%] → [0.000000, 1296.724320]
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__tmp_chauf_mUATxVdkin0/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__tmp_chauf_mUATxVdkin0/tmp_olay.nii
++ User-entered function range value value (0.6)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 27 32 27
++ 3dAutobox: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Auto bbox: x=24…168 y=25…205 z=6…160
++ 3dAutobox: output dataset = QC_sub-11481002_ses-1/media/__tmp_chauf_mUATxVdkin0/ulay_box_0.nii
++ 3dmaskdump: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=QC_sub-11481002_ses-1/media/tmp_chauf_mUATxVdkin0/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_XYZ-eIRwActSAV7ufadOXrJBg argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /tmp/3dcalc_XYZ
-eIRwActSAV7ufadOXrJBg+tlrc.BRIK
++ 4067975 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ How many coors? 3
++ Will have the ref box central coors : SET_DICOM_XYZ 1 17 5
++ Will have the ref box central gapord: 20 25 22

------------------- end of optionizing -------------------

– trying to start Xvfb :279
[1] 17724
+/gpfs/data/sfeldste/ImagingData/Study/MINA/MINA_BIDS/sub-11481002/ses-1/derivatives/REST/sub-11481002_ses-1.results/QC_sub-11481002_ses-1/media/__tmp_chauf_mUATxVdkin0++ Writing palette image to QC_sub-11481002_ses-1/media/qc_05_vstat_seed_lh-cort-aud.pbar.jpg
++ Writing one 3218x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_05_vstat_seed_lh-cort-aud.sag.jpg’
++ Writing one 2714x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_05_vstat_seed_lh-cort-aud.cor.jpg’
++ Writing one 2714x458 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_05_vstat_seed_lh-cort-aud.axi.jpg’

AFNI QUITTs!

+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=7x1:20:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=7x1:25:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=7x1:22:1:black crop=0:0,0:0 -com SET_PBAR_ALL -99 1 Reds_and_Blues_Inv -com PBAR_SAVEIM QC_sub-11481002_ses-1/media/qc_05_vstat_seed_lh-cort-aud.pbar.jpg dim=64x512H -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1296.724320 -com SET_FUNC_RANGE 0.6 -com SET_THRESHNEW 0.3 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 1 17 5 -com SAVE_JPEG sagittalimage QC_sub-11481002_ses-1/media/qc_05_vstat_seed_lh-cort-aud.sag blowup=2 -com SAVE_JPEG coronalimage QC_sub-11481002_ses-1/media/qc_05_vstat_seed_lh-cort-aud.cor blowup=2 -com SAVE_JPEG axialimage QC_sub-11481002_ses-1/media/qc_05_vstat_seed_lh-cort-aud.axi blowup=2 -com QUITT QC_sub-11481002_ses-1/media/__tmp_chauf_mUATxVdkin0

+* Removing temporary image directory ‘QC_sub-11481002_ses-1/media/__tmp_chauf_mUATxVdkin0’.

[1] + Done Xvfb :279 -screen 0 1024x768x24

++ DONE (good exit)
see: QC_sub-11481002_ses-1/media/qc_05_vstat_seed_lh-cort-aud*

Traceback (most recent call last):
File “/gpfs/runtime/opt/afni/21.2.04/1dplot.py”, line 50, in
from afnipy import lib_plot_1D as lpod
File “/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_plot_1D.py”, line 39, in
import matplotlib.pyplot as plt
ImportError: No module named matplotlib.pyplot
Traceback (most recent call last):
File “/gpfs/runtime/opt/afni/21.2.04/1dplot.py”, line 50, in
from afnipy import lib_plot_1D as lpod
File “/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_plot_1D.py”, line 39, in
import matplotlib.pyplot as plt
ImportError: No module named matplotlib.pyplot
++ 3dGrayplot: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]

  • Loading dataset ./errts.sub-11481002_ses-1.anaticor+tlrc.HEAD
  • Number of voxels in mask = 235612
  • 3dGrayplot: Elapsed = 100.8 s
    ++ pbar name has known extension: jpg
    ++ My command:
    @chauffeur_afni -ulay full_mask.sub-11481002_ses-1+tlrc.HEAD -olay full_mask.sub-11481002_ses-1+tlrc.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar gray_scale -func_range 3.29 -blowup 1 -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_sub-11481002_ses-1/media/qc_08_mot_grayplot.pbar.jpg -pbar_comm_range for normal distr, bounds of 0.001 prob tail -prefix __tmp_ZXCV_img -save_ftype JPEG -montx 1 -monty 1 -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean

++ Using AFNI ver : AFNI_21.2.04
++ chauffeur ver : 6.26

------------------ start of optionizing ------------------

++ Found input file: full_mask.sub-11481002_ses-1+tlrc.HEAD
++ Found input file: full_mask.sub-11481002_ses-1+tlrc.HEAD
++ Using blowup factor: 1
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ./__tmp_chauf_EuuDLfrQsPm
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user’s range:
++ Ulay to be visualized within user range:
[0%, 98%] → [0.000000, 1.000000]
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_EuuDLfrQsPm/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_EuuDLfrQsPm/tmp_olay.nii
++ User-entered function range value value (3.29)
++ Dimensions (xyzt): 96 114 96 1
++ (initial) Slice spacing ordered (x,y,z) is: 96 114 96
++ 3dAutomask: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Emperor Zhark
++ 3dAutobox: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Auto bbox: x=0…95 y=0…113 z=0…95
++ THD_zeropad: all pad values are zero - just copying dataset
++ 3dAutobox: output dataset = ./__tmp_chauf_EuuDLfrQsPm/ulay_box_0.nii
++ 3dmaskdump: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=./__tmp_chauf_EuuDLfrQsPm/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_XYZ_022m9urTgULmnO1cF-GXJA argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0: no scale factor
++ Computing output statistics
++ Output dataset /tmp/3dcalc_XYZ_022m9urTgULmnO1cF-GXJA+tlrc.BRIK
++ 1050624 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ How many coors? 3
++ Will have the ref box central coors : SET_DICOM_XYZ 1 19 19
++ Will have the ref box central gapord: 96 114 96

------------------- end of optionizing -------------------

– trying to start Xvfb :170
[1] 18183
+/gpfs/data/sfeldste/ImagingData/Study/MINA/MINA_BIDS/sub-11481002/ses-1/derivatives/REST/sub-11481002_ses-1.results/__tmp_chauf_EuuDLfrQsPm++ Writing palette image to QC_sub-11481002_ses-1/media/qc_08_mot_grayplot.pbar.jpg
++ Writing one 114x96 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > ./__tmp_ZXCV_img.sag.jpg’
++ Writing one 96x96 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > ./__tmp_ZXCV_img.cor.jpg’
++ Writing one 96x114 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > ./__tmp_ZXCV_img.axi.jpg’

AFNI QUITTs!

+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=1x1:96:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=1x1:114:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=1x1:96:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 1 gray_scale -com PBAR_SAVEIM QC_sub-11481002_ses-1/media/qc_08_mot_grayplot.pbar.jpg dim=64x512H -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 3.29 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 1 19 19 -com SAVE_JPEG sagittalimage ./__tmp_ZXCV_img.sag blowup=1 -com SAVE_JPEG coronalimage ./__tmp_ZXCV_img.cor blowup=1 -com SAVE_JPEG axialimage ./__tmp_ZXCV_img.axi blowup=1 -com QUITT ./__tmp_chauf_EuuDLfrQsPm

+* Removing temporary image directory ‘./__tmp_chauf_EuuDLfrQsPm’.

[1] + Done Xvfb :170 -screen 0 1024x768x24

++ DONE (good exit)
see: ./__tmp_ZXCV_img*

Traceback (most recent call last):
File “/gpfs/runtime/opt/afni/21.2.04/1dplot.py”, line 50, in
from afnipy import lib_plot_1D as lpod
File “/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_plot_1D.py”, line 39, in
import matplotlib.pyplot as plt
ImportError: No module named matplotlib.pyplot
** ERROR: pnmcat – not found in path – @djunct_glue_imgs_vert fails
** WARNING: this script cannot run without installing package netpbm11
rm: cannot remove ‘__tmp_img_enorm.jpg’: No such file or directory
++ Check summary of degrees of freedom in: QC_sub-11481002_ses-1/media/qc_09_regr_df.dat
++ olay_alpha has known value: Yes
++ pbar name has known extension: jpg
++ My command:
@chauffeur_afni -ulay /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz -box_focus_slices /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz -olay corr_brain+tlrc.HEAD -cbar Reds_and_Blues_Inv -ulay_range 0% 120% -func_range 0.6 -thr_olay 0.3 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_sub-11481002_ses-1/media/qc_10_regr_corr_errts.pbar.jpg -pbar_comm_range Pearson r -pbar_comm_thr alpha+boxed on -prefix QC_sub-11481002_ses-1/media/qc_10_regr_corr_errts -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean

++ Using AFNI ver : AFNI_21.2.04
++ chauffeur ver : 6.26

------------------ start of optionizing ------------------

++ Found input file: /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
++ Found input file: corr_brain+tlrc.HEAD
++ Found focus refbox file: /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
+* NB: focus box vol has >1 slice, so we select [0]th.
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_sub-11481002_ses-1/media/__tmp_chauf_YXAoQ2xhSqu
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user’s range:
++ Ulay range calc for >100%ile ulay max:
calculating 98%ile value, and then
multiplying it by a scale factor = 1.22448,
in order to produce the 98%ile value
++ Ulay to be visualized within user range:
[0%, 120%] → [0.000000, 1296.724320]
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__tmp_chauf_YXAoQ2xhSqu/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__tmp_chauf_YXAoQ2xhSqu/tmp_olay.nii
++ User-entered function range value value (0.6)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 27 32 27
++ 3dAutobox: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Auto bbox: x=24…168 y=25…205 z=6…160
++ 3dAutobox: output dataset = QC_sub-11481002_ses-1/media/__tmp_chauf_YXAoQ2xhSqu/ulay_box_0.nii
++ 3dmaskdump: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=QC_sub-11481002_ses-1/media/__tmp_chauf_YXAoQ2xhSqu/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_XYZ_AEkz-o0BerSY8C22AqiQ1Q argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /tmp/3dcalc_XYZ_AEkz-o0BerSY8C22AqiQ1Q+tlrc.BRIK
++ 4067975 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ How many coors? 3
++ Will have the ref box central coors : SET_DICOM_XYZ 1 17 5
++ Will have the ref box central gapord: 20 25 22

------------------- end of optionizing -------------------

– trying to start Xvfb :894
[1] 18459
+/gpfs/data/sfeldste/ImagingData/Study/MINA/MINA_BIDS/sub-11481002/ses-1/derivatives/REST/sub-11481002_ses-1.results/QC_sub-11481002_ses-1/media/__tmp_chauf_YXAoQ2xhSqu++ Writing palette image to QC_sub-11481002_ses-1/media/qc_10_regr_corr_errts.pbar.jpg
++ Writing one 3218x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_10_regr_corr_errts.sag.jpg’
++ Writing one 2714x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_10_regr_corr_errts.cor.jpg’
++ Writing one 2714x458 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_10_regr_corr_errts.axi.jpg’

AFNI QUITTs!

+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=7x1:20:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=7x1:25:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=7x1:22:1:black crop=0:0,0:0 -com SET_PBAR_ALL -99 1 Reds_and_Blues_Inv -com PBAR_SAVEIM QC_sub-11481002_ses-1/media/qc_10_regr_corr_errts.pbar.jpg dim=64x512H -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1296.724320 -com SET_FUNC_RANGE 0.6 -com SET_THRESHNEW 0.3 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 1 17 5 -com SAVE_JPEG sagittalimage QC_sub-11481002_ses-1/media/qc_10_regr_corr_errts.sag blowup=2 -com SAVE_JPEG coronalimage QC_sub-11481002_ses-1/media/qc_10_regr_corr_errts.cor blowup=2 -com SAVE_JPEG axialimage QC_sub-11481002_ses-1/media/qc_10_regr_corr_errts.axi blowup=2 -com QUITT QC_sub-11481002_ses-1/media/__tmp_chauf_YXAoQ2xhSqu

+* Removing temporary image directory ‘QC_sub-11481002_ses-1/media/__tmp_chauf_YXAoQ2xhSqu’.

[1] + Done Xvfb :894 -screen 0 1024x768x24

++ DONE (good exit)
see: QC_sub-11481002_ses-1/media/qc_10_regr_corr_errts*

++ Prepare for running adjunct_apqc_tsnr_general (ver = 1.1)
++ MODE: 10
++ olay_alpha has known value: No
*+ Setting pbar file extension: jpg

++ My command:
@chauffeur_afni -ulay /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz -olay TSNR.sub-11481002_ses-1+tlrc.HEAD -ulay_range 0% 120% -func_range 481 -box_focus_slices /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz -set_subbricks 0 0 0 -pbar_posonly -blowup 2 -cbar 481=red 422=oran-red 363=orange 304=oran-yell 245=yell-oran 186=yellow 128=lt-blue2 66=blue 0=none -cbar_ncolors 8 -cbar_topval EMPTY -opacity 4 -olay_alpha No -olay_boxed No -thr_olay 0 -pbar_saveim QC_sub-11481002_ses-1/media/qc_11_regr_tsnr_fin.pbar -pbar_comm_range 95%ile in mask -pbar_comm_gen cbar: hot color range (5-95%ile TSNR in mask): 128 - 481 -prefix QC_sub-11481002_ses-1/media/qc_11_regr_tsnr_fin -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass -pass

++ Using AFNI ver : AFNI_21.2.04
++ chauffeur ver : 6.26

------------------ start of optionizing ------------------

++ Found input file: /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
++ Found input file: TSNR.sub-11481002_ses-1+tlrc.HEAD
++ Found focus refbox file: /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
+* NB: focus box vol has >1 slice, so we select [0]th.
++ Using blowup factor: 2
++ Using opacity: 4
++ Making temporary work directory to copy vis files: QC_sub-11481002_ses-1/media/__tmp_chauf_gLm15eUtnAm
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user’s range:
++ Ulay range calc for >100%ile ulay max:
calculating 98%ile value, and then
multiplying it by a scale factor = 1.22448,
in order to produce the 98%ile value
++ Ulay to be visualized within user range:
[0%, 120%] → [0.000000, 1296.724320]
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__tmp_chauf_gLm15eUtnAm/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-11481002_ses-1/media/__tmp_chauf_gLm15eUtnAm/tmp_olay.nii
++ User-entered function range value value (481)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 27 32 27
++ 3dAutobox: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Auto bbox: x=24…168 y=25…205 z=6…160
++ 3dAutobox: output dataset = QC_sub-11481002_ses-1/media/__tmp_chauf_gLm15eUtnAm/ulay_box_0.nii
++ 3dmaskdump: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=QC_sub-11481002_ses-1/media/__tmp_chauf_gLm15eUtnAm/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_XYZ_4-xvYVLPFupem6_CMU2_oA argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /tmp/3dcalc_XYZ_4-xvYVLPFupem6_CMU2_oA+tlrc.BRIK
++ 4067975 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ How many coors? 3
++ Will have the ref box central coors : SET_DICOM_XYZ 1 17 5
++ Will have the ref box central gapord: 20 25 22

------------------- end of optionizing -------------------

– trying to start Xvfb :743
[1] 18763
+/gpfs/data/sfeldste/ImagingData/Study/MINA/MINA_BIDS/sub-11481002/ses-1/derivatives/REST/sub-11481002_ses-1.results/QC_sub-11481002_ses-1/media/__tmp_chauf_gLm15eUtnAm++ Writing palette image to QC_sub-11481002_ses-1/media/qc_11_regr_tsnr_fin.pbar.jpg
++ Writing one 3218x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_11_regr_tsnr_fin.sag.jpg’
++ Writing one 2714x386 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_11_regr_tsnr_fin.cor.jpg’
++ Writing one 2714x458 image to filter ‘/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > QC_sub-11481002_ses-1/media/qc_11_regr_tsnr_fin.axi.jpg’

AFNI QUITTs!

+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=4 mont=7x1:20:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=7x1:25:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=7x1:22:1:black crop=0:0,0:0 -com SET_PBAR_ALL +8 481=red 422=oran-red 363=orange 304=oran-yell 245=yell-oran 186=yellow 128=lt-blue2 66=blue 0=none -com PBAR_SAVEIM QC_sub-11481002_ses-1/media/qc_11_regr_tsnr_fin.pbar.jpg dim=64x512H -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1296.724320 -com SET_FUNC_RANGE 481 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 1 17 5 -com SAVE_JPEG sagittalimage QC_sub-11481002_ses-1/media/qc_11_regr_tsnr_fin.sag blowup=2 -com SAVE_JPEG coronalimage QC_sub-11481002_ses-1/media/qc_11_regr_tsnr_fin.cor blowup=2 -com SAVE_JPEG axialimage QC_sub-11481002_ses-1/media/qc_11_regr_tsnr_fin.axi blowup=2 -com QUITT QC_sub-11481002_ses-1/media/__tmp_chauf_gLm15eUtnAm

+* Removing temporary image directory ‘QC_sub-11481002_ses-1/media/__tmp_chauf_gLm15eUtnAm’.

[1] + Done Xvfb :743 -screen 0 1024x768x24

++ DONE (good exit)
see: QC_sub-11481002_ses-1/media/qc_11_regr_tsnr_fin*

++ Check for corr matrix warnings in: QC_sub-11481002_ses-1/media/qc_12_warns_xmat.dat
++ Check for censor fraction warnings (general): QC_sub-11481002_ses-1/media/qc_13_warns_cen_total.dat
++ Check basic summary quants from proc in: QC_sub-11481002_ses-1/media/qc_15_qsumm_ssrev.dat

+++++++++++ Check output of @ss_review_basic +++++++++++

subject ID : sub-11481002_ses-1
AFNI version : AFNI_21.2.04
AFNI package : linux_openmp_64
TR : 0.8
TRs removed (per run) : 6
num stim classes provided : 0
final anatomy dset : anat_final.sub-11481002_ses-1+tlrc.HEAD
final stats dset : NO_STATS
final errts dset : errts.sub-11481002_ses-1.anaticor+tlrc.HEAD
orig voxel counts : 90 90 60
orig voxel resolution : 2.400000 2.400000 2.400000
orig volume center : 3.332405 -13.407387 2.108025
final voxel resolution : 2.000000 2.000000 2.000000

motion limit : 0.2
num TRs above mot limit : 0
average motion (per TR) : 0.0658111
average censored motion : 0.0658111
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
max motion displacement : 0.640088
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
max censored displacement : 0.640088
outlier limit : 0.1
average outlier frac (TR) : 0.000315133
num TRs above out limit : 0

/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
num runs found : 2
num TRs per run : 377 377
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
num TRs per run (applied) : 377 377
num TRs per run (censored): 0 0
fraction censored per run : 0 0
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
TRs total (uncensored) : 754
TRs total : 754
degrees of freedom used : 20
degrees of freedom left : 734

/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
TRs censored : 0
censor fraction : 0.000000
num regs of interest : 0

TSNR average : 306.941
global correlation (GCOR) : 0.0493667
anat/EPI mask Dice coef : 0.950105
anat/templ mask Dice coef : 0.977062
blur estimates (ACF) : 0.835231 5.4437 11.6187
blur estimates (FWHM) : 0 0 0

#!/bin/tcsh

This script is meant to help review single subject results.

This script should be run from a ‘.results’ directory produced by an

afni_proc.py processing script.

It generates an HTML file of useful QC information (images + text) of the

data throughout its processing. Results for this subject are stored in

‘QC_sub-11481002_ses-1’ and may be viewed using an standard browser, e.g.:

firefox QC_sub-11481002_ses-1/index.html

The script can be re-run. Variables are defined in the ‘Top level’ section

and used throughout, but otherwise the script is modular. individual

sections can be run with or without modification (e.g., copying them into

a new file), as long as the ‘Top level’ sections are all present.

================== Top level: file names and global vars ===================

set subj = sub-11481002_ses-1
set afni_ver = AFNI_21.2.04
set afni_package = linux_openmp_64
set nt_orig = 754
set nt_applied = 754
set tr = 0.8
set rm_trs = 6
set num_stim = 0
set tcat_dset = pb00.sub-11481002_ses-1.r01.tcat+orig.HEAD
set censor_dset = censor_sub-11481002_ses-1_combined_2.1D
set enorm_dset = motion_sub-11481002_ses-1_enorm.1D
set motion_dset = dfile_rall.1D
set volreg_dset = pb04.sub-11481002_ses-1.r01.volreg+tlrc.HEAD
set outlier_dset = outcount_rall.1D
set gcor_dset = out.gcor.1D
set mask_corr_dset = out.mask_ae_dice.txt
set mask_anat_templ_corr_dset = out.mask_at_dice.txt
set mot_limit = 0.2
set out_limit = 0.1
set xmat_regress = X.xmat.1D
set xmat_uncensored = X.nocensor.xmat.1D
set stats_dset = NO_STATS
set sum_ideal = sum_baseline.1D
set align_anat = sub-11481002_ses-1_al_keep+orig.HEAD
set final_anat = anat_final.sub-11481002_ses-1+tlrc.HEAD
set vr_base_dset = vr_base_min_outlier+orig.HEAD
set final_epi_dset = final_epi_vr_base_min_outlier+tlrc.HEAD
set final_view = tlrc
set template = MNI152_2009_template_SSW.nii.gz
set mask_dset = full_mask.sub-11481002_ses-1+tlrc.HEAD
set tsnr_dset = TSNR.sub-11481002_ses-1+tlrc.HEAD
set errts_dset = errts.sub-11481002_ses-1.anaticor+tlrc.HEAD
set ss_review_dset = out.ss_review.sub-11481002_ses-1.txt
set df_info_dset = out.df_info.txt
set cormat_warn_dset = out.cormat_warn.txt
set pre_ss_warn_dset = out.pre_ss_warn.txt

================ Top level: make output directory structure ================

pretty self explanatory

set odir_qc = QC_${subj}
set odir_img = ${odir_qc}/media
set odir_info = ${odir_qc}/extra_info

\mkdir -p ${odir_img}
\mkdir -p ${odir_info}

======================== Top level: find main dset =========================

Find the main dset, mostly for ulay functionality,

in descending order of preference:

template, anat_final, vr_base.

try to locate the template as main dset

set btemp = basename ${template}
set templ_path = @FindAfniDsetPath ${template}

if ( ${#templ_path} ) then
set main_dset = “${templ_path}/${btemp}”
echo “*+ Found main dset (template): ${main_dset}”
else
# try to find dset by basename only
set templ_path = @FindAfniDsetPath ${btemp}

if ( ${#templ_path} ) then
    set main_dset = "${templ_path}/${btemp}"
    echo "*+ Found main dset (template) on 2nd try:  ${main_dset}"
else
    echo "** ERROR: Cannot find template, though one was specified."
    echo "   Please put the template in a findable spot, and try again."
    exit 1
endif

endif

set main_dset_sp = 3dinfo -space ${main_dset}

========================== Top level: censor info ==========================

Check the censoring

set cstr = 1d_tool.py -show_trs_censored encoded -infile ${censor_dset}
set Ncstr = 1d_tool.py -verb 0 -show_censor_count -infile ${censor_dset}
set Pcstr = echo "scale=0; ${Ncstr} * 100 / ${nt_orig}" | bc
if ( echo "${Ncstr} > 0" | bc && “${Pcstr}” == “0” ) then
set Pcstr = “<1”
endif

set rep_cen_str = “censored vols (${Pcstr}%): ${cstr}”
set addtxt_cen_str = " and combined censoring"

set cen_have_mot = 1
set ytop_mot = echo "3 * ${mot_limit}" | bc

set cen_have_out = 1
set ytop_out = echo "3 * ${out_limit}" | bc

set cen_color = ‘red’
set cen_hline_color = ‘cyan’
set cen_cmd = “-censor_files ${censor_dset}”
set cen_lim_mot = “-censor_hline ${mot_limit}”
set cen_lim_mot_yax = “-yaxis 0:${ytop_mot}”
set cen_lim_out = “-censor_hline ${out_limit}”
set cen_lim_out_yax = “-yaxis 0:${ytop_out}”
set cen_lim_all = “-censor_hline ${mot_limit} ${out_limit}”
set cen_lim_all_yax = “-yaxis 0:${ytop_mot} 0:${ytop_out}”

================== Top level: sundry pieces for multi-use ==================

Setup sundry useful bits of info

set ssrev_ln = grep "num TRs per run" ${ss_review_dset} | grep -v "("
set pats = “${ssrev_ln[6-]}”

========================= title of html page: subj =========================

subject ID for html page title

set opref = __page_title
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.json

cat << EOF >! ${tjson}
itemtype :: TITLE
itemid :: pagetop
blockid :: Top
blockid_hov :: Top of page for:&#10${subj}
title :: afni_proc.py single subject report
subj :: “${subj}”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

============================ EPI in orig space =============================

Check the quality of acquired EPI in orig space (ulay) 98 %ile topval for

pbar

set opref = qc_00_vorig_EPI
set ulay = “${vr_base_dset}”
set ulay_name = 3dinfo -prefix ${vr_base_dset}
set ulay_ob = 3dinfo -obliquity ${vr_base_dset}
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.axi.json
set tjson2 = _tmp2.txt
set ojson2 = ${odir_img}/${opref}.sag.json
set opbarrt = ${odir_img}/${opref}.pbar

set minmax = 3dBrickStat \ -slow \ -min -max \ ${ulay}

set pp = 3dBrickStat \ -slow \ -percentile 98 1 98 \ ${ulay}

set olay_topval = ${pp[2]}
set olay_botval = 0

@chauffeur_afni
-ulay ${ulay}
-olay ${ulay}
-ulay_range_nz 0 ${olay_topval}
-func_range ${olay_topval}
-box_focus_slices AMASK_FOCUS_ULAY
-cbar gray_scale
-pbar_posonly
-pbar_saveim “${opbarrt}.jpg”
-pbar_comm_range “98%ile in vol”
-pbar_for “dset”
-prefix “${odir_img}/${opref}”
-save_ftype JPEG
-blowup 4
-opacity 9
-montx 7 -monty 1
-montgap 1
-montcolor ‘black’
-set_xhairs OFF
-label_mode 1 -label_size 3
-do_clean

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input “${opbarrt}.txt”
-prefix “${opbarrt}.json”

cat << EOF >! ${tjson}
itemtype :: VOL
itemid :: EPI
blockid :: vorig
blockid_hov :: vols in orig space
title :: Check vols in original space
text :: “EPI in original space (volreg base)” , “dset: ${ulay_name} (EPI)”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

cat << EOF >! ${tjson2}
itemtype :: VOL
itemid :: EPI
blockid :: vorig
blockid_hov :: vols in orig space
title :: Check vols in original space
subtext :: “SHOW_PBAR:${opref}.pbar.json” , “range: [${minmax[1]}, ${minmax[2]}]; obliquity: ${ulay_ob}”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson2}
-prefix ${ojson2}

======================= EPI and anatomical alignment =======================

Compare the quality of alignment between the anatomical (ulay) and

edge-ified EPI (olay):

look at gross alignment

follow ventricles and gyral patterns

set opref = qc_01_ve2a_epi2anat
set focus_box = ${main_dset}
set ulay_name = 3dinfo -prefix ${final_epi_dset}
set olay_name = 3dinfo -prefix ${final_anat}
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.axi.json
set tjson2 = _tmp2.txt
set ojson2 = ${odir_img}/${opref}.sag.json

@djunct_edgy_align_check
-olay ${final_anat}
-box_focus_slices ${focus_box}
-ulay ${final_epi_dset}
-use_olay_grid wsinc5
-ulay_range_nz “2%” “98%”
-prefix ${odir_img}/${opref}

cat << EOF >! ${tjson}
itemtype :: VOL
itemid :: epi2anat
blockid :: ve2a
blockid_hov :: vol alignment (EPI-anat)
title :: Check vol alignment (EPI to anat)
text :: “ulay: ${ulay_name} (EPI)” , “olay: ${olay_name} (anat edges)”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

cat << EOF >! ${tjson2}
itemtype :: VOL
itemid :: epi2anat
blockid :: ve2a
blockid_hov :: vol alignment (EPI-anat)
title :: Check vol alignment (EPI to anat)
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson2}
-prefix ${ojson2}

==================== anatomical and template alignment =====================

Compare the quality of alignment between the template (ulay) and

edge-ified anatomical (olay):

look at gross alignment

follow ventricles and gyral patterns

set opref = qc_02_va2t_anat2temp
set focus_box = ${main_dset}
set ulay_name = 3dinfo -prefix ${final_anat}
set olay_name = 3dinfo -prefix ${main_dset}
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.axi.json
set tjson2 = _tmp2.txt
set ojson2 = ${odir_img}/${opref}.sag.json

@djunct_edgy_align_check
-ulay ${final_anat}
-box_focus_slices ${focus_box}
-olay ${main_dset}
-prefix ${odir_img}/${opref}

cat << EOF >! ${tjson}
itemtype :: VOL
itemid :: anat2temp
blockid :: va2t
blockid_hov :: vol alignment (anat-template)
title :: Check vol alignment (anat to template)
text :: “ulay: ${ulay_name} (anat)” , “olay: ${olay_name} (template edges, ${main_dset_sp} space)”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

cat << EOF >! ${tjson2}
itemtype :: VOL
itemid :: anat2temp
blockid :: va2t
blockid_hov :: vol alignment (anat-template)
title :: Check vol alignment (anat to template)
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson2}
-prefix ${ojson2}

======================= view seedbased corr: lh-PCC ========================

check seedbased corr results:

errts vol: ${errts_dset}

seed name: lh-PCC

set opref = qc_03_vstat_seed_lh-PCC
set ulay_dset = ${main_dset}
set focus_box = ${main_dset}
set ulay_name = 3dinfo -prefix ${ulay_dset}
set olay_name = 3dinfo -prefix ${errts_dset}
set voxvol = 3dinfo -voxvol ${errts_dset}
set seed_rad = echo "${voxvol}" | awk '{printf "%0.2f",(2*($1)^0.3334);}'
set t1dfile = _tmp_ave_ts.txt
set tcorrvol = _tmp_corr_vol.nii
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.axi.json
set tjson2 = _tmp2.txt
set ojson2 = ${odir_img}/${opref}.sag.json
set opbarrt = ${odir_img}/${opref}.pbar

3dmaskave
-quiet
-dball 5.0 49.0 40.0 ${seed_rad}
${errts_dset}
> ${t1dfile}

3dTcorr1D
-overwrite
-prefix ${tcorrvol}
${errts_dset}
${t1dfile}

@chauffeur_afni
-ulay ${ulay_dset}
-box_focus_slices ${focus_box}
-olay ${tcorrvol}
-cbar Reds_and_Blues_Inv
-ulay_range 0% 120%
-func_range 0.6
-thr_olay 0.3
-olay_alpha Yes
-olay_boxed Yes
-set_subbricks 0 0 0
-opacity 9
-pbar_saveim “${opbarrt}.jpg”
-pbar_comm_range “Pearson r”
-pbar_comm_thr “alpha+boxed on”
-prefix “${odir_img}/${opref}”
-save_ftype JPEG
-montx 7 -monty 1
-montgap 1
-montcolor ‘black’
-set_xhairs OFF
-label_mode 1 -label_size 3
-do_clean

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input “${opbarrt}.txt”
-prefix “${opbarrt}.json”

cat << EOF >! ${tjson}
itemtype :: VOL
itemid :: seed_lh-PCC
blockid :: vstat
blockid_hov :: statistics vols
title :: Check statistics vols (and effect estimates)
text :: “olay: seed-based corr map (in ${olay_name})” , “seed: ‘lh-PCC’ in DMN, rad = ${seed_rad} mm (5.0L, 49.0P, 40.0S)”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

cat << EOF >! ${tjson2}
itemtype :: VOL
itemid :: seed_lh-PCC
blockid :: vstat
blockid_hov :: statistics vols
title :: Check statistics vols (and effect estimates)
subtext :: “SHOW_PBAR:${opref}.pbar.json”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson2}
-prefix ${ojson2}

===================== view seedbased corr: rh-cort-vis =====================

check seedbased corr results:

errts vol: ${errts_dset}

seed name: rh-cort-vis

set opref = qc_04_vstat_seed_rh-cort-vis
set ulay_dset = ${main_dset}
set focus_box = ${main_dset}
set ulay_name = 3dinfo -prefix ${ulay_dset}
set olay_name = 3dinfo -prefix ${errts_dset}
set voxvol = 3dinfo -voxvol ${errts_dset}
set seed_rad = echo "${voxvol}" | awk '{printf "%0.2f",(2*($1)^0.3334);}'
set t1dfile = _tmp_ave_ts.txt
set tcorrvol = _tmp_corr_vol.nii
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.axi.json
set tjson2 = _tmp2.txt
set ojson2 = ${odir_img}/${opref}.sag.json
set opbarrt = ${odir_img}/${opref}.pbar

3dmaskave
-quiet
-dball -4.0 91.0 -3.0 ${seed_rad}
${errts_dset}
> ${t1dfile}

3dTcorr1D
-overwrite
-prefix ${tcorrvol}
${errts_dset}
${t1dfile}

@chauffeur_afni
-ulay ${ulay_dset}
-box_focus_slices ${focus_box}
-olay ${tcorrvol}
-cbar Reds_and_Blues_Inv
-ulay_range 0% 120%
-func_range 0.6
-thr_olay 0.3
-olay_alpha Yes
-olay_boxed Yes
-set_subbricks 0 0 0
-opacity 9
-pbar_saveim “${opbarrt}.jpg”
-pbar_comm_range “Pearson r”
-pbar_comm_thr “alpha+boxed on”
-prefix “${odir_img}/${opref}”
-save_ftype JPEG
-montx 7 -monty 1
-montgap 1
-montcolor ‘black’
-set_xhairs OFF
-label_mode 1 -label_size 3
-do_clean

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input “${opbarrt}.txt”
-prefix “${opbarrt}.json”

cat << EOF >! ${tjson}
itemtype :: VOL
itemid :: seed_rh-cort-vis
blockid :: vstat
blockid_hov :: statistics vols
title :: Check statistics vols (and effect estimates)
text :: “olay: seed-based corr map (in ${olay_name})” , “seed: ‘rh-cort-vis’ in Vis, rad = ${seed_rad} mm (4.0R, 91.0P, 3.0I)”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

cat << EOF >! ${tjson2}
itemtype :: VOL
itemid :: seed_rh-cort-vis
blockid :: vstat
blockid_hov :: statistics vols
title :: Check statistics vols (and effect estimates)
subtext :: “SHOW_PBAR:${opref}.pbar.json”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson2}
-prefix ${ojson2}

===================== view seedbased corr: lh-cort-aud =====================

check seedbased corr results:

errts vol: ${errts_dset}

seed name: lh-cort-aud

set opref = qc_05_vstat_seed_lh-cort-aud
set ulay_dset = ${main_dset}
set focus_box = ${main_dset}
set ulay_name = 3dinfo -prefix ${ulay_dset}
set olay_name = 3dinfo -prefix ${errts_dset}
set voxvol = 3dinfo -voxvol ${errts_dset}
set seed_rad = echo "${voxvol}" | awk '{printf "%0.2f",(2*($1)^0.3334);}'
set t1dfile = _tmp_ave_ts.txt
set tcorrvol = _tmp_corr_vol.nii
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.axi.json
set tjson2 = _tmp2.txt
set ojson2 = ${odir_img}/${opref}.sag.json
set opbarrt = ${odir_img}/${opref}.pbar

3dmaskave
-quiet
-dball 64.0 12.0 2.0 ${seed_rad}
${errts_dset}
> ${t1dfile}

3dTcorr1D
-overwrite
-prefix ${tcorrvol}
${errts_dset}
${t1dfile}

@chauffeur_afni
-ulay ${ulay_dset}
-box_focus_slices ${focus_box}
-olay ${tcorrvol}
-cbar Reds_and_Blues_Inv
-ulay_range 0% 120%
-func_range 0.6
-thr_olay 0.3
-olay_alpha Yes
-olay_boxed Yes
-set_subbricks 0 0 0
-opacity 9
-pbar_saveim “${opbarrt}.jpg”
-pbar_comm_range “Pearson r”
-pbar_comm_thr “alpha+boxed on”
-prefix “${odir_img}/${opref}”
-save_ftype JPEG
-montx 7 -monty 1
-montgap 1
-montcolor ‘black’
-set_xhairs OFF
-label_mode 1 -label_size 3
-do_clean

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input “${opbarrt}.txt”
-prefix “${opbarrt}.json”

cat << EOF >! ${tjson}
itemtype :: VOL
itemid :: seed_lh-cort-aud
blockid :: vstat
blockid_hov :: statistics vols
title :: Check statistics vols (and effect estimates)
text :: “olay: seed-based corr map (in ${olay_name})” , “seed: ‘lh-cort-aud’ in Aud, rad = ${seed_rad} mm (64.0L, 12.0P, 2.0S)”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

cat << EOF >! ${tjson2}
itemtype :: VOL
itemid :: seed_lh-cort-aud
blockid :: vstat
blockid_hov :: statistics vols
title :: Check statistics vols (and effect estimates)
subtext :: “SHOW_PBAR:${opref}.pbar.json”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson2}
-prefix ${ojson2}

================ mot enorm plus outlier frac, and censoring ================

review plots (colored TRs are censored); outliers with enorm motion limit

set jpgsize = 1600
set opref = qc_06_mot_enormoutlr
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.json

1dplot.py
-boxplot_on
-patches ${pats}
-colors black
-infiles “${enorm_dset}” “${outlier_dset}”
-ylabels “enorm (~mm)” “outlier frac”
${cen_cmd}
${cen_lim_all_yax}
${cen_lim_all}
-xlabel “vol index”
-title “Mot enorm and outlier frac (black), with limit (${cen_hline_color}) and combined censoring (${cen_color})”
-prefix “${odir_img}/${opref}.jpg”

cat << EOF >! ${tjson}
itemtype :: 1D
itemid :: enormoutlr
blockid :: mot
blockid_hov :: motion and outliers
title :: Check motion and outliers
text :: Motion Euclidean norm (enorm) and outlier fraction , with limit and combined censoring
subtext :: “${rep_cen_str}”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

==================== volreg motion pars, and censoring =====================

review plots: 3dvolreg motion regressors

set jpgsize = 1600
set opref = qc_07_mot_VR6
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.json

1dplot.py
-sepscl
-boxplot_on
-patches ${pats}
-reverse_order
-infiles “${motion_dset}”
-ylabels VOLREG
${cen_cmd}
-xlabel “vol index”
-title “Estimated motion parameters (volreg), with combined censoring (${cen_color} bars)”
-prefix “${odir_img}/${opref}.jpg”

cat << EOF >! ${tjson}
itemtype :: 1D
itemid :: VR6
blockid :: mot
blockid_hov :: motion and outliers
title :: Check motion and outliers
text :: 6 volume registration motion parameters (in ${motion_dset}) , with combined censoring
subtext :: “${rep_cen_str}”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

======================== make grayplot of residuals ========================

grayplot of residuals … with enorm plot

set opref = qc_08_mot_grayplot
set errts_name = 3dinfo -prefix ${errts_dset}
set mask_name = 3dinfo -prefix ${mask_dset}
set tmpvol_pref = __tmp_ZXCV_img
set tmp_gplot = __tmp_ZXCV_gplot.jpg
set opbarrt = ${odir_img}/${opref}.pbar
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.json
set tmp_img = __tmp_img_enorm.jpg

3dGrayplot
-polort -1
-pvorder
-dimen 1800 500
-range 3.29
-input ${errts_dset}
-mask ${mask_dset}
-prefix ${tmp_gplot}

@chauffeur_afni
-ulay ${mask_dset}
-olay ${mask_dset}
-box_focus_slices AMASK_FOCUS_OLAY
-cbar gray_scale
-func_range 3.29
-blowup 1
-set_subbricks 0 0 0
-opacity 9
-pbar_saveim “${opbarrt}.jpg”
-pbar_comm_range “for normal distr, bounds of 0.001 prob tail”
-prefix “${tmpvol_pref}”
-save_ftype JPEG
-montx 1 -monty 1
-set_xhairs OFF
-label_mode 1 -label_size 3
-do_clean

1dplot.py
-margin_off
-one_graph
-figsize 12 0.5
-dpi 150
-patches ${pats}
-infiles “${enorm_dset}” “${outlier_dset}”
-scale SCALE_TO_HLINE
-yaxis 0:3
${cen_cmd}
${cen_lim_all}
-colors blue green
-prefix ${tmp_img}

@djunct_glue_imgs_vert
-imbot ${tmp_gplot}
-imtop ${tmp_img}
-prefix ${odir_img}/${opref}.jpg

\rm ${tmpvol_pref}*jpg
\rm ${tmp_gplot}
\rm ${tmp_img}

cat << EOF >! ${tjson}
itemtype :: 1D
itemid :: grayplot
blockid :: mot
blockid_hov :: motion and outliers
title :: Check motion and outliers
text :: “Grayplot (‘-pvorder’) of residuals dset: ${errts_name}”,“top: motion enorm (blue) and outlier frac (green), with censoring (${cen_color})”
subtext :: “SHOW_PBAR:${opref}.pbar.json” , " rows: ordered by similarity to top two principal comps in mask (${mask_name})"
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input “${opbarrt}.txt”
-prefix “${opbarrt}.json”

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

========================= check degrees of freedom =========================

df check for processing

set opref = qc_09_regr_df
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.json

1d_tool.py -show_df_info -infile ${xmat_regress}
> ${odir_img}/${opref}.dat

echo “++ Check summary of degrees of freedom in: ${odir_img}/${opref}.dat”

cat << EOF >! ${tjson}
itemtype :: DAT
itemid :: df
blockid :: regr
blockid_hov :: regressors
title :: Check regressors, DFs and residuals
text :: “Summary of degrees of freedom (DF) usage from processing”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

==================== check ave errts corr through brain ====================

check ave errts (in WB mask) corr throughout dset:

corr brain dset: corr_brain+tlrc.HEAD

set opref = qc_10_regr_corr_errts
set ulay_dset = ${main_dset}
set focus_box = ${main_dset}
set olay_dset = corr_brain+tlrc.HEAD
set ulay_name = 3dinfo -prefix ${ulay_dset}
set olay_name = 3dinfo -prefix ${olay_dset}
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.axi.json
set tjson2 = _tmp2.txt
set ojson2 = ${odir_img}/${opref}.sag.json
set opbarrt = ${odir_img}/${opref}.pbar

@chauffeur_afni
-ulay ${ulay_dset}
-box_focus_slices ${focus_box}
-olay ${olay_dset}
-cbar Reds_and_Blues_Inv
-ulay_range 0% 120%
-func_range 0.6
-thr_olay 0.3
-olay_alpha Yes
-olay_boxed Yes
-set_subbricks 0 0 0
-opacity 9
-pbar_saveim “${opbarrt}.jpg”
-pbar_comm_range “Pearson r”
-pbar_comm_thr “alpha+boxed on”
-prefix “${odir_img}/${opref}”
-save_ftype JPEG
-montx 7 -monty 1
-montgap 1
-montcolor ‘black’
-set_xhairs OFF
-label_mode 1 -label_size 3
-do_clean

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input “${opbarrt}.txt”
-prefix “${opbarrt}.json”

cat << EOF >! ${tjson}
itemtype :: VOL
itemid :: corr_errts
blockid :: regr
blockid_hov :: regressors
title :: Check regressors, DFs and residuals
text :: “olay: corr of WB-average errts with each voxel (${olay_name})”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

cat << EOF >! ${tjson2}
itemtype :: VOL
itemid :: corr_errts
blockid :: regr
blockid_hov :: regressors
title :: Check regressors, DFs and residuals
subtext :: “SHOW_PBAR:${opref}.pbar.json”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson2}
-prefix ${ojson2}

============================= check final TSNR =============================

TSNR: 5-95%ile range in mask_dset highlighted

set opref = qc_11_regr_tsnr_fin
set ulay_dset = ${main_dset}
set olay_dset = ${tsnr_dset}
set focus_box = ${main_dset}
set ulay_name = 3dinfo -prefix ${ulay_dset}
set olay_name = 3dinfo -prefix ${olay_dset}
set avsp = 3dinfo -av_space ${olay_dset}
set olaylabel = 3dinfo -label ${olay_dset}
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.axi.json
set tjson2 = _tmp2.txt
set ojson2 = ${odir_img}/${opref}.sag.json
set opbarrt = ${odir_img}/${opref}.pbar
set mask_name = 3dinfo -prefix ${mask_dset}

adjunct_apqc_tsnr_general
-ulay ${ulay_dset}
-olay ${olay_dset}
-focus ${focus_box}
-mask ${mask_dset}
-prefix ${odir_img}/${opref}
-prefix_cbar ${opbarrt}

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input “${opbarrt}.txt”
-prefix “${opbarrt}.json”

cat << EOF >! ${tjson}
itemtype :: VOL
itemid :: tsnr_fin
blockid :: regr
blockid_hov :: regressors
title :: Check regressors, DFs and residuals
text :: “olay: ${olay_name} (final TSNR dset)” , “mask: ${mask_name} (for percentile range)”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

cat << EOF >! ${tjson2}
itemtype :: VOL
itemid :: tsnr_fin
blockid :: regr
blockid_hov :: regressors
title :: Check regressors, DFs and residuals
subtext :: “SHOW_PBAR:${opref}.pbar.json”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson2}
-prefix ${ojson2}

=========================== correlation warnings ===========================

review: check for correlation matrix warnings

set opref = qc_12_warns_xmat
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.json

1d_tool.py
-show_cormat_warnings
-infile ${xmat_regress}
> ${odir_img}/${opref}.dat

echo “++ Check for corr matrix warnings in: ${odir_img}/${opref}.dat”

cat << EOF >! ${tjson}
itemtype :: WARN
itemid :: xmat
blockid :: warns
blockid_hov :: all warnings from processing
title :: Check all warnings from processing
text :: “Regression matrix correlation warnings”
warn_level :: none
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

========================= Censor fraction (total) ==========================

review: check for df warnings due to censoring

set opref = qc_13_warns_cen_total
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.json

echo “++ Check for censor fraction warnings (general): ${odir_img}/${opref}.dat”

echo “Censored 0 of 754 total time points : 0.0%\n” > ${odir_img}/${opref}.dat

cat << EOF >! ${tjson}
itemtype :: WARN
itemid :: cen_total
blockid :: warns
blockid_hov :: all warnings from processing
title :: Check all warnings from processing
text :: “General censor fraction warnings”
warn_level :: none
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

======================== pre-steady state warnings =========================

review: check for pre-steady state warnings

set opref = qc_14_warns_press
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.json

if ( -f ${pre_ss_warn_dset} && ! -z ${pre_ss_warn_dset} ) then
cat ${pre_ss_warn_dset} > ${odir_img}/${opref}.dat
else
printf “” > ${odir_img}/${opref}.dat
endif

cat << EOF >! ${tjson}
itemtype :: WARN
itemid :: press
blockid :: warns
blockid_hov :: all warnings from processing
title :: Check all warnings from processing
text :: “Pre-steady state warnings”
warn_level :: none
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

=========================== ss review basic info ===========================

summary quantities from processing

set opref = qc_15_qsumm_ssrev
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.json

cat out.ss_review.${subj}.txt
> ${odir_img}/${opref}.dat

echo “++ Check basic summary quants from proc in: ${odir_img}/${opref}.dat”

cat << EOF >! ${tjson}
itemtype :: DAT
itemid :: ssrev
blockid :: qsumm
blockid_hov :: summary quantities from @ss_review_basic
title :: Check summary quantities from @ss_review_basic
text :: “Basic summary quantities from processing”
EOF

abids_json_tool.py
-overwrite
-txt2json
-delimiter_major ‘::’
-delimiter_minor ‘,’
-input ${tjson}
-prefix ${ojson}

======================== copy JSONs over to QC dir =========================

preserve subj jsons

set all_jsons = ( out.ss_review_uvars.json
)

foreach ff ( ${all_jsons} )
\cp ${ff} ${odir_info}/.
end

================== copy review basic text file to QC dir ===================

preserve subj review_basic text file

\cp ${ss_review_dset} ${odir_info}/.

==================== ss review basic info to terminal ====================

basic information from processing

echo “”
echo “”
echo “# +++++++++++ Check output of @ss_review_basic +++++++++++ #”
echo “”

cat ${ss_review_dset}

====================== Finish gracefully, if possible ======================

exit 0

It looks like you don’t have the Matplotlib module installed:


 Traceback (most recent call last):
File "/gpfs/runtime/opt/afni/21.2.04/1dplot.py", line 50, in <module>
from afnipy import lib_plot_1D as lpod
File "/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_plot_1D.py", line 39, in <module>
import matplotlib.pyplot as plt
ImportError: No module named matplotlib.pyplot
Traceback (most recent call last):
File "/gpfs/runtime/opt/afni/21.2.04/1dplot.py", line 50, in <module>
from afnipy import lib_plot_1D as lpod
File "/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_plot_1D.py", line 39, in <module>
import matplotlib.pyplot as plt
ImportError: No module named matplotlib.pyplot 

What is the output of:


afni_system_check.py -check_all

?

–pt

-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-1062.el7.x86_64
version: #1 SMP Thu Jul 18 20:25:13 UTC 2019
distribution: Red Hat Enterprise Linux Server 7.7 Maipo
number of CPUs: 24
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /gpfs/runtime/opt/afni/21.2.04/afni
afni version : Precompiled binary linux_openmp_64: Jul 28 2021
: AFNI_21.2.04 ‘Nerva’
AFNI_version.txt : AFNI_21.2.04, linux_openmp_64, Jul 28 2021
which python : /gpfs/runtime/opt/python/2.7.12/bin/python
python version : 2.7.5
which R : which: no R in (/gpfs/runtime/opt/Xvfb/1.20.12/bin:/gpfs/runtime/opt/afni/21.2.04:/gpfs/runtime/opt/intel/2017.0/bin:/gpfs/runtime/opt/python/2.7.12/bin:/gpfs/runtime/opt/matlab/R2017b/bin:/gpfs/runtime/opt/java/8u111/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/usr/lpp/mmfs/sbin:/opt/ibutils/bin:/gpfs/runtime/bin:/users/bhyun2/bin)

which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/gpfs/rt/7.2/opt/afni/21.2.04/afni)
R : 0
python : 2
/gpfs/rt/7.2/opt/python/2.7.12/bin/python2.7
/usr/bin/python2.7
python2 : 2
/gpfs/rt/7.2/opt/python/2.7.12/bin/python2.7
/usr/bin/python2.7
python3 : 0

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE
R: Command not found.

R RHOME : R: Command not found.

checking for $HOME files…
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib64/python2.7/site-packages/PyQt4/init.pyc

** failed to load module matplotlib.pyplot
– matplotlib.pyplot is not required, but is desirable

-------------------------------- env vars --------------------------------
PATH = /gpfs/runtime/opt/Xvfb/1.20.12/bin:/gpfs/runtime/opt/afni/21.2.04:/gpfs/runtime/opt/intel/2017.0/bin:/gpfs/runtime/opt/python/2.7.12/bin:/gpfs/runtime/opt/matlab/R2017b/bin:/gpfs/runtime/opt/java/8u111/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/usr/lpp/mmfs/sbin:/opt/ibutils/bin:/gpfs/runtime/bin:/users/bhyun2/bin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /gpfs/runtime/opt/libjpeg/9.0/lib:/gpfs/runtime/opt/gsl/1.15/lib:/gpfs/runtime/opt/libpng12/1.2.57/lib:/gpfs/runtime/opt/netpbm/10.47.71/lib:/gpfs/runtime/opt/python/3.9.0/lib:/gpfs/runtime/opt/intel/2017.0/lib/intel64:/gpfs/runtime/opt/intel/2017.0/mkl/lib/intel64:/gpfs/runtime/opt/java/8u111/jre/lib/amd64

DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /gpfs/runtime/opt/afni/21.2.04

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3

========================= summary, please fix: =========================

  • just be aware: login shell ‘bash’, but our code examples use ‘tcsh’
  • failure under initial “AFNI and related program tests”
  • missing R packages (see rPkgsInstall)
  • please run: cp /gpfs/runtime/opt/afni/21.2.04/AFNI.afnirc ~/.afnirc
  • please run: “suma -update_env” for .sumarc
  • please run: apsearch -update_all_afni_help
  • insufficient data for AFNI bootcamp

I do have it installed now, what would be the easiest way to generate that one image, or will the whole QC html generation need to be done again?

OK, great.

To rerun the APQC HTML generation for one or more ‘results’ directories, you can get this script (to redo the APQC pythonically) anywhere:


curl -O [https://raw.githubusercontent.com/afni/afni/master/src/ptaylor/supplement/redo_apqc.tcsh](https://raw.githubusercontent.com/afni/afni/master/src/ptaylor/supplement/redo_apqc.tcsh)

and then run it providing one or more locations of *.results directories, such as:


tcsh redo_apqc.tcsh  DIR1  DIR2  DIR3  DIR4 ...

The script will go to each directory, move any existing QC_/ directory to old_QC_/, and re-run the APQC HTML-generating steps to generate a new QC*/.

I would try it out on 1 results directory first just to make sure all is in order, and then loop over as many others as you would like.

Please let me know how that goes.

–pt

From the start I am getting these errors, and no index file is generated at the end

++ REDOing APQC
++ Going to re-run APQC in this many dirs: 1
Traceback (most recent call last):
File “/gpfs/runtime/opt/python/3.9.0/lib/python3.9/subprocess.py”, line 73, in
import msvcrt
ModuleNotFoundError: No module named ‘msvcrt’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/gpfs/runtime/opt/afni/21.2.04/apqc_make_tcsh.py”, line 189, in
from afnipy import lib_apqc_tcsh as lat
File “/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_apqc_tcsh.py”, line 186, in
import subprocess
File “/gpfs/runtime/opt/python/3.9.0/lib/python3.9/subprocess.py”, line 78, in
import _posixsubprocess
ImportError: dynamic module does not define module export function (PyInit__posixsubprocess)
+ Found main dset (template): /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print('
* uncensor from vec: nt = %d, but nocen len = %d’
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
Traceback (most recent call last):
File “/gpfs/runtime/opt/python/3.9.0/lib/python3.9/subprocess.py”, line 73, in
import msvcrt
ModuleNotFoundError: No module named ‘msvcrt’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/gpfs/runtime/opt/afni/21.2.04/abids_json_tool.py”, line 19, in
import sys, os, glob, subprocess, csv, re, argparse, signal, textwrap, json
File “/gpfs/runtime/opt/python/3.9.0/lib/python3.9/subprocess.py”, line 78, in
import _posixsubprocess

I have never seen these errors before, and unfortunately don’t have a RedHat linux to test anything on.

It looks like some kind of Python conflict, perhaps? The afni_system_check.py lists only Python 2.* versions that it can find:


python : 2
/gpfs/rt/7.2/opt/python/2.7.12/bin/python2.7
/usr/bin/python2.7
python2 : 2
/gpfs/rt/7.2/opt/python/2.7.12/bin/python2.7
/usr/bin/python2.7
python3 : 0

However, in your $PATH (and in the error messages of running Python here) it refers to Python3:


Traceback (most recent call last):
File "/gpfs/runtime/opt/python/3.9.0/lib/python3.9/subprocess.py", line 73, in <module>
import msvcrt
ModuleNotFoundError: No module named 'msvcrt'

Oddly, that ‘msvcrt’ seems to be a windows-specific package.

This helpfile suggested making a soft link:
https://stackoverflow.com/questions/66814603/pip-is-not-working-error-no-module-named-msvcrt
but I am not sure if/how that would help. I am a little perplexed about which Python version is being used. The afni_system_check.py seems to think it is:


python version : 2.7.5

What does “which python” output? (I assume it is 2.7.5?)

–pt

Thanks for looking into this. I am using python 3.9.0 currently and I am not sure if that is causing the conflict?

Going through the outputs looking for just the mot_grayplot.jpg

I do see these errors

++ FOR: outcount_rall.1D: 1 arrays with 754 pts
*+ No ylabels entered
*+ No input x-axis; making values based on length of data: [0…753]
++ Will scale each time series by censor_hline
++ Apply scale: 5.0
++ Apply scale: 10.0
++ Will apply same y-axis range ‘[0.0, 3.0]’ to all dsets
++ Plotting:
++ Plotting:
Traceback (most recent call last):
File “/gpfs/runtime/opt/afni/21.2.04/1dplot.py”, line 65, in
ok_fig = lpod.make_1dplot_figure(bigfig)
File “/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_plot_1D.py”, line 495, in make_1dplot_figure
plt.savefig( bf.fname, dpi=bf.dpi, facecolor=bf.bkgd_color)
File “/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/pyplot.py”, line 695, in savefig
res = fig.savefig(*args, **kwargs)
File “/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/figure.py”, line 2062, in savefig
self.canvas.print_figure(fname, **kwargs)
File “/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py”, line 2173, in print_figure
canvas = self._get_output_canvas(format)
File “/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py”, line 2105, in _get_output_canvas
.format(fmt, ", ".join(sorted(self.get_supported_filetypes()))))
ValueError: Format ‘jpg’ is not supported (supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz)
djpeg: can’t open __tmp_img_enorm.jpg
pnmcat: Error reading magic number from Netpbm image stream. Most often, this means your input file is empty.
Empty input file

+* Removing temporary files ‘__tmp_gluing*’

++ DONE! Image output:
QC_sub-11481001_ses-1/media/qc_08_mot_grayplot.jpg

Hi-

It looks like your system might be missing libjpeg to be able to create JPGs:


ValueError: Format 'jpg' is not supported (supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz)

Searching for available libjpeg versions on Centos 7:


yum search libjpeg

… it looks like the following would be the way to do it on a 64-bit system:


sudo yum install libjpeg-turbo.x86_64

Does that install it, so that JPGs can be made?

–pt

The some of the errors were taken care of after I reverted to python 2.7.12
Using matplotlib 2.2.4
libjpeg-turbo 2.0.2

I am still getting this error for the qc_08_grayplot

_ses-1_enorm.1D: 1 arrays with 754 pts
++ FOR: outcount_rall.1D: 1 arrays with 754 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0…753]
++ Plotting: enorm (~mm)
++ Plotting: outlier frac
Traceback (most recent call last):
File “/gpfs/runtime/opt/afni/21.2.04/1dplot.py”, line 65, in
ok_fig = lpod.make_1dplot_figure(bigfig)
File “/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_plot_1D.py”, line 498, in make_1dplot_figure
bbox_inches=‘tight’)
File “/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/pyplot.py”, line 695, in savefig
res = fig.savefig(*args, **kwargs)
File “/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/figure.py”, line 2062, in savefig
self.canvas.print_figure(fname, **kwargs)
File “/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py”, line 2173, in print_figure
canvas = self._get_output_canvas(format)
File “/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py”, line 2105, in _get_output_canvas
.format(fmt, ", ".join(sorted(self.get_supported_filetypes()))))
ValueError: Format ‘jpg’ is not supported (supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz)
++ FOR: dfile_rall.1D: 6 arrays with 754 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0…753]
++ Plotting: dP
(mm)
++ Plotting: dL
(mm)
++ Plotting: dS
(mm)
++ Plotting: yaw
(deg)
++ Plotting: pitch
(deg)
++ Plotting: roll
(deg)
Traceback (most recent call last):
File “/gpfs/runtime/opt/afni/21.2.04/1dplot.py”, line 65, in
ok_fig = lpod.make_1dplot_figure(bigfig)
File “/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_plot_1D.py”, line 498, in make_1dplot_figure
bbox_inches=‘tight’)
File “/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/pyplot.py”, line 695, in savefig
res = fig.savefig(*args, **kwargs)
File “/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/figure.py”, line 2062, in savefig
self.canvas.print_figure(fname, **kwargs)
File “/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py”, line 2173, in print_figure
canvas = self._get_output_canvas(format)
File “/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py”, line 2105, in _get_output_canvas
.format(fmt, ", ".join(sorted(self.get_supported_filetypes()))))
ValueError: Format ‘jpg’ is not supported (supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz)

The pbar, seems to be written out fine

media/qc_08_mot_grayplot.pbar.jpg
++ Writing one 114x96 image to filter ‘/gpfs/runtime/opt/libjpeg-turbo/2.0.2/bin/cjpeg -quality 95 > ./__tmp_ZXCV_img.sag.jpg’
++ Writing one 96x96 image to filter ‘/gpfs/runtime/opt/libjpeg-turbo/2.0.2/bin/cjpeg -quality 95 > ./__tmp_ZXCV_img.cor.jpg’
++ Writing one 96x114 image to filter ‘/gpfs/runtime/opt/libjpeg-turbo/2.0.2/bin/cjpeg -quality 95 > ./__tmp_ZXCV_img.axi.jpg’

OK, clooooser…

When I made a conda environment to setup various versions of Python:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/miniconda.html#make-basic-conda-environments
… I had to include the “pillow” module, too, for Python 2.7; this was the way the module is setup (I just find ipython and numpy useful, they shouldn’t be necessary here):


conda create -y                 \
      -n py27_afni_tiny         \
      python=2.7                \
      matplotlib numpy          \
      pillow ipython

The “pillow” module is the updated version of the old PIL (Python Image Library). Can you install python-pillow on that system?

–pt

Thanks, I do see the missing images, but not sure how to resolve the formatting errors at the very end

average censored motion : 0.0600584
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
max motion displacement : 1.31744
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
max censored displacement : 1.31744
outlier limit : 0.1
average outlier frac (TR) : 0.000652547
num TRs above out limit : 0

/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
num runs found : 2
num TRs per run : 377 377
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
num TRs per run (applied) : 366 375
num TRs per run (censored): 11 2
fraction censored per run : 0.0291777 0.00530504
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_afni1D.py:1302: SyntaxWarning: ‘str’ object is not callable; perhaps you missed a comma?
print(‘** uncensor from vec: nt = %d, but nocen len = %d’
TRs total (uncensored) : 754

Hmm, clooooooooser…

That is odd. The last time I saw that warning, it ended up being a server error:
https://afni.nimh.nih.gov/afni/community/board/read.php?1,166118,166275#msg-166275

Also, the “perhaps you missed a comma” message seems to be something that was added in Python 3.8, so I wouldn’t expect to see it in Python 2.7 execution.

Can you please try running the “redo” script again, and then send me the contents of the “out.review_html” file again?

Sorry this is such a hassle…

–pt

+ Found main dset (template): /gpfs/runtime/opt/afni/21.2.04/MNI152_2009_template_SSW.nii.gz
^[[7m
+ WARNING:^[[0m If you are performing spatial transformations on an oblique dset,
such as ./vr_base_min_outlier+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./vr_base_min_outlier+orig.BRIK is 3.600054 degrees from plumb.
^[[7m*+ WARNING:^[[0m If you are performing spatial transformations on an oblique dset,
such as ./vr_base_min_outlier+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./vr_base_min_outlier+orig.BRIK is 3.600054 degrees from plumb.
++ pbar name has known extension: jpg
++ My command:
@chauffeur_afni -ulay vr_base_min_outlier+orig.HEAD -olay vr_base_min_outlier+orig.HEAD -ulay_range_nz 0 355.364746 -func_range 355.364746 -box_focus_slices AMASK_FOCUS_ULAY -cbar gray_scale -pbar_posonly -pbar_saveim QC_sub-11481001_ses-1/media/qc_00_vorig_EPI.pbar.jpg -pbar_comm_range 98%ile in vol -pbar_for dset -prefix QC_sub-11481001_ses-1/media/qc_00_vorig_EPI -save_ftype JPEG -blowup 4 -opacity 9 -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean

++ Using AFNI ver : AFNI_21.2.04
++ chauffeur ver : 6.26

------------------ start of optionizing ------------------

++ Found input file: vr_base_min_outlier+orig.HEAD
++ Found input file: vr_base_min_outlier+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_sub-11481001_ses-1/media/__tmp_chauf_DWNEN3By1fU
++ Converted 0 to labels
++ Final subbrick indices: -1 -1 -1
++ Copy ulay to visualize (volumetric) within user’s range:
++ Ulay to be visualized within user range:
[0, 355.364746]
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
“out.review_html” 1012L, 62599C

Hi-

I don’t think that’s the complete out.review_html file, is it? Could you perhaps email it to me—again, it is giant to post.

–pt

This issue never has a resolution posted here, unfortunately, but in seeing something similar again, we have resolved what was probably happening. A post about it actually exists here.

What seems to be happening is that a particular version of Matplotlib (3.1.2) has a known error about producing JPGs. Unfortunately, the Aptitude package manager in Ubuntu 20.04 by default installs exactly this version by default, so users who have used something like sudo apt-get install python3-matplotlib to install Python in Ubuntu 20.04 will likely have this issue. To check your Python's Matplotlib version number, you can run:

python -c "import matplotlib as mmm; print(mmm.__version__)"

If it comes out as "3.1.2", you will likely not be able to make JPG images successfully from Matplotlib, causing a few parts of the APQC HTML to be missing (those that use 1dplot.py, specifically).

To resolve this issue, you can install a different version of Matplotlib as follows:

sudo apt-get install pip
sudo apt-get remove python3-matplotlib
pip install matplotlib

--pt