no png after fat_proc_axialize_anat

charujing123 · December 17, 2018, 3:00pm

Hi
After running the program, there was no PNG in the anat_01.
Here is the program I used.

I/O path, same as above; just need the “proc” dirs now

set path_P_ss = /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001

reference anatomical volumes to which we axialize

set here = $PWD/fatcat_proc_mni_ref
set ref_t2w = $here/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE.nii.gz
set ref_t2w_wt = $here/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE_wtell.nii.gz

fat_proc_axialize_anat
-inset $path_P_ss/anat_00/s005a1001.nii
-prefix $path_P_ss/anat_01/t1w
-mode_t1w
-refset $ref_t2w
-extra_al_wtmask $ref_t2w_wt
-out_match_ref

ptaylor · December 17, 2018, 3:07pm

What is your operating system?

–pt

charujing123 · December 18, 2018, 12:01am

Hi Paul
The OS is MACOS mojave 10.14

ptaylor · December 18, 2018, 2:25pm

Having an error message and/or output of the program would be useful here…

Perhaps the netpbm installation was not successful earlier, and so PNGs are not being written? Please try this:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html#install-netpbm
from the installation instructions, and let us know what happens.

–pt

charujing123 · December 18, 2018, 2:56pm

hi paul, i think the netpbm is already in my macos.

bash-3.2$ brew install netpbm
Warning: netpbm 10.73.22 is already installed and up-to-date
To reinstall 10.73.22, run `brew reinstall netpbm`

Here is the output in the command during running the

"# I/O path, same as above; just need the “proc” dirs now
set path_P_ss = /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001

reference anatomical volumes to which we axialize

set here = $PWD/fatcat_proc_mni_ref
set ref_t2w = $here/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE.nii.gz
set ref_t2w_wt = $here/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE_wtell.nii.gz

fat_proc_axialize_anat
-inset $path_P_ss/anat_00/s005a1001.nii
-prefix $path_P_ss/anat_01/t1w
-mode_t1w
-refset $ref_t2w
-extra_al_wtmask $ref_t2w_wt
-out_match_ref -extra_al_opts “-newgrid 1.0”
"

CMac:scripts caroline$ tcsh dti_proc
++ Start script version: 4.2
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
118
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Found input file: /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_00/s005a1001.nii
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Found input file: /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE.nii.gz
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Found input file: /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE_wtell.nii.gz

++ Based on prefix, the output directory will be:
/Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01
++ Based on prefix, the output prefix will be:
t1w

+* WARNING: Somehow found a premade working directory (?):
/Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w
NB: will not clean it afterwards.
\n-----> STARTING ---->
\n\nThis command:
fat_proc_axialize_anat -inset /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_00/s005a1001.nii -prefix /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/t1w -mode_t1w -refset /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE.nii.gz -extra_al_wtmask /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE_wtell.nii.gz -out_match_ref -extra_al_opts -newgrid 1.0\n\n
++ Echoing the command to: /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/t1w_cmd.txt
\nThe reference template is: /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE.nii.gz

+++ Command Echo:
3dresample -orient AIL -prefix /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF.nii -inset /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE.nii.gz -overwrite

+++ Command Echo:
3drefit -space ORIG -view orig /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF.nii

++ 3drefit: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF.nii

loading and re-writing dataset /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF.nii (/Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF.nii in NIFTI storage)
++ 3drefit processed 1 datasets

+++ Command Echo:
3dresample -orient AIL -prefix /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF_WT.nii -inset /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE_wtell.nii.gz -overwrite

+++ Command Echo:
3drefit -space ORIG -view orig /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF_WT.nii

++ 3drefit: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF_WT.nii

loading and re-writing dataset /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF_WT.nii (/Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF_WT.nii in NIFTI storage)
++ 3drefit processed 1 datasets

+++ Command Echo:
3dcalc -a /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_00/s005a1001.nii -expr a -prefix /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/tt_00.nii -float -overwrite

++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/tt_00.nii
++ Distance between input’s center of mass to (0,0,0) is 46.16598 mm.
→ if this is large, you might want to recenter with:
3dCM -set 0 0 0 FILE
or something (you could copy it first).
\n\n++ Threshold value at 90%: 476.000000\n

+++ Command Echo:
3dcalc -a tt_00.nii -expr maxbelow(476.000000,a) -prefix tt_01_thr.nii -overwrite

++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./tt_01_thr.nii
\n++ Doing unifizing.

+++ Command Echo:
3dUnifize -echo_edu -GM -prefix tt_02_uni.nii -input tt_01_thr.nii -overwrite

++ 3dUnifize: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]

Pre-processing: ADV…UWGm
++ Output dataset ./tt_02_uni.nii
++ ===== CPU time = 99.3 sec Elapsed = 29.2
\n\n++ Percentile for thresholding: 1198.538086\n

+++ Command Echo:
3dcalc -a tt_02_uni.nii -expr maxbelow(1198.538086,a) -prefix tt_03_thr2.nii -overwrite

++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./tt_03_thr2.nii
++ processing tt_03_thr2.nii …

+++ Command Echo:
3dAllineate -1Dmatrix_save _map_lr6 -warp shift_rotate -prefix tt_05_LR6.nii -base tt_04_LRflip.nii -twopass -cost nmi -source tt_03_thr2.nii -overwrite

++ 3dAllineate: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./tt_03_thr2.nii
++ Base dataset: ./tt_04_LRflip.nii
++ Loading datasets
++ 4614769 voxels in source_automask+0
++ Zero-pad: xbot=3 xtop=0
++ Zero-pad: ybot=4 ytop=0
++ Zero-pad: zbot=4 ztop=4
++ Computing -autobox
++ 8887424 voxels [81.8%] in weight mask
++ Number of points for matching = 4177089
++ master dataset for output = base
++ OpenMP thread count = 6
++ ======= Allineation of 1 sub-bricks using Normalized MI [H(b,s)/(H(b)+H(s))] =======
++ *** Coarse pass begins ***
++ *** Fine pass begins ***

Final fine fit Parameters:
x-shift= 3.0378 y-shift= 0.2042 z-shift= 0.4294
z-angle= 4.5462 x-angle= -0.3741 y-angle= -8.8608
++ Output dataset ./tt_05_LR6.nii
++ Wrote -1Dmatrix_save _map_lr6.aff12.1D
++ 3dAllineate: total CPU time = 468.7 sec Elapsed = 217.0
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################

+++ Command Echo:
3dAllineate -1Dmatrix_apply _map_lr_half.aff12.1D -prefix tt_06_LRmid.nii -source tt_03_thr2.nii -final wsinc5 -overwrite

++ 3dAllineate: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./tt_03_thr2.nii
++ Base dataset: (not given)
++ You might want to use ‘-master’ when using ‘-1D*_apply’
++ Loading datasets
++ master dataset for output = source
++ OpenMP thread count = 6
++ ========== 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 ./tt_06_LRmid.nii
++ 3dAllineate: total CPU time = 22.6 sec Elapsed = 4.6
++ ###########################################################
++ New inp0 = tt_07_origLR.nii

+++ Command Echo:
3dAllineate -1Dmatrix_apply _map_lr_half.aff12.1D -prefix tt_07_origLR.nii -source tt_00.nii -final wsinc5 -overwrite

++ 3dAllineate: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./tt_00.nii
++ Base dataset: (not given)
++ You might want to use ‘-master’ when using ‘-1D*_apply’
++ Loading datasets
++ master dataset for output = source
++ OpenMP thread count = 6
++ ========== 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 ./tt_07_origLR.nii
++ 3dAllineate: total CPU time = 22.5 sec Elapsed = 4.5
++ ###########################################################
++ Aligning center of inset → refset.
*+ WARNING: Over-writing dataset ./tt_06_LRmid.nii
++ Wrote new dataset: ./tt_06_LRmid.nii
base: 0.507591 20.3921 11.2511
dset: 3.76337 -21.7929 -48.2708
delta: -3.255779 42.185000 59.521900
42.185000 59.521900 3.255779
++ 3drefit: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./tt_07_origLR.nii
deoblique
loading and re-writing dataset ./tt_07_origLR.nii (./tt_07_origLR.nii in NIFTI storage)
++ 3drefit processed 1 datasets

+++ Command Echo:
3dAllineate -1Dparam_save _map_9dof -warp shift_rotate_scale -prefix tt_08_alnd.nii -base REF.nii -twopass -source_automask -weight REF_WT.nii -wtprefix tt_08_wtmask.nii -cost lpa -source tt_06_LRmid.nii -overwrite

++ 3dAllineate: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./tt_06_LRmid.nii
++ Base dataset: ./REF.nii
++ Loading datasets
++ 4456775 voxels in -source_automask
++ Zero-pad: ybot=3 ytop=0
++ 2227632 voxels [28.1%] in weight mask
++ Output dataset ./tt_08_wtmask.nii
++ Number of points for matching = 1046987
++ Local correlation: blok type = ‘RHDD(6.54321)’
++ master dataset for output = base
++ OpenMP thread count = 6
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Abs =======
++ *** Coarse pass begins ***
++ *** Fine pass begins ***

Final fine fit Parameters:
x-shift= -0.1258 y-shift= 11.0985 z-shift= 35.4955
z-angle= -0.5371 x-angle= 6.5675 y-angle= -0.1284
x-scale= 1.0493 y-scale= 0.9702 z-scale= 0.9082
++ Output dataset ./tt_08_alnd.nii
++ Wrote -1Dparam_save _map_9dof.param.1D
++ 3dAllineate: total CPU time = 146.2 sec Elapsed = 50.6
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################
++ # ‘-autoweight’ is recommended when using -lpc or -lpa #
++ # If your results are not good, please try again. #
++ ###########################################################

+++ Command Echo:
3dAllineate -1Dparam_apply map_fake12dof.param.1D -prefix tt_09_alnd0.nii -source tt_07_origLR.nii -final wsinc5 -newgrid 1.0 -master REF.nii -overwrite

++ 3dAllineate: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./tt_07_origLR.nii
++ Base dataset: (not given)
++ Loading datasets
++ changing output grid spacing to 1.0000 mm
++ OpenMP thread count = 6
++ ========== 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 ./tt_09_alnd0.nii
++ 3dAllineate: total CPU time = 15.1 sec Elapsed = 3.2
++ ###########################################################

+++ Command Echo:
3dcalc -overwrite -a tt_09_alnd0.nii -expr a -prefix …/t1w.nii.gz

++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./…/t1w.nii.gz
++ Making QC images.
++ QC image 00 (final output ulay): t1w_qc_xlzd
++ My command:
@chauffeur_afni -ulay …/t1w.nii.gz -prefix …/QC/t1w_qc_xlzd -montx 3 -monty 3 -set_xhairs MULTI -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
+* Noting: you did NOT provide an overlay, and yet
you did NOT turn off the overlay with ‘-olay_off’
→ so I assume you just want to view the underlay.
++ Using blowup factor: 2
++ Using opacity: 6
++ Making temporary work directory to copy vis files: …/QC/__tmp_chauf_J2dMGFqIb7v
++ Copy ulay to visualize (volumetric) within user’s range:
++ Ulay to be visualized within user range:
[0%, 98%] → [0.000000, 570.249207]
++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./…/QC/__tmp_chauf_J2dMGFqIb7v/tmp_ulay.nii
++ No overlay viewing
++ Dimensions (xyzt): 236 172 192 1
++ (initial) Slice spacing ordered (x,y,z) is: 21 26 19
++ 3dmaskdump: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ 7793664 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 117 85 95
\n------------------- end of optionizing -------------------\n
– trying to start Xvfb :81
[1] 65074
Precompiled binary macos_10.12_local: Dec 5 2018 (Version AFNI_18.3.15 ‘Augustus’)

+++ Command Echo:
afni -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_ulay.nii -com SEE_OVERLAY - -com SET_PBAR_ALL -99 1 Plasma -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 570.249207 -com SET_FUNC_RANGE 0 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS MULTI -com OPEN_WINDOW sagittalimage opacity=6 mont=3x3:21 crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=6 mont=3x3:26 crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=6 mont=3x3:19 crop=0:0,0:0 -com SET_IJK 117 85 95 -com SAVE_PNG sagittalimage …/QC/t1w_qc_xlzd.sag blowup=2 -com SAVE_PNG coronalimage …/QC/t1w_qc_xlzd.cor blowup=2 -com SAVE_PNG axialimage …/QC/t1w_qc_xlzd.axi blowup=2 -com QUITT …/QC/__tmp_chauf_J2dMGFqIb7v

Thanks go to KR Hammett for great efforts

Initializing: X11[The X.Org Foundation v 11804000].
*** can’t get X11 colormap entry for overlay color ###
*** can’t get X11 colormap entry for overlay color for
*** can’t get X11 colormap entry for overlay color underlay
*** can’t get X11 colormap entry for overlay color AFNI_GLOBAL_SESSION. Widgets… Input files:
session # 1 = QC/__tmp_chauf_J2dMGFqIb7v/ ==> 1 dataset
dataset count = 1
Time series = 5 files read
Plugins = 0 libraries read
++ Writing one 1416x1032 image to filter ‘/usr/local/bin/pnmtopng -compression 9 > …/QC/t1w_qc_xlzd.sag.png’
++ Writing one 1152x1032 image to filter ‘/usr/local/bin/pnmtopng -compression 9 > …/QC/t1w_qc_xlzd.cor.png’
++ Writing one 1152x1416 image to filter ‘/usr/local/bin/pnmtopng -compression 9 > …/QC/t1w_qc_xlzd.axi.png’

AFNI QUITTs!
\n+* Removing temporary image directory ‘…/QC/__tmp_chauf_J2dMGFqIb7v’.\n
[1] Done Xvfb :81 -screen 0 1024x768x24
++ QC image 01 (earlier allin olaying ref ulay): t1w_qc_ref_in
++ 3dedge3: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ My command:
@chauffeur_afni -ulay REF.nii -ulay_range 2% 98% -olay ./tt_alnd_edges.nii -func_range_perc_nz 50 -pbar_posonly -cbar red_monochrome -opacity 6 -prefix …/QC/t1w_qc_ref_in -montx 3 -monty 3 -set_xhairs MULTI -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Using blowup factor: 2
++ Using opacity: 6
++ Making temporary work directory to copy vis files: …/QC/__tmp_chauf_aOV7ti8h37D
++ Copy ulay to visualize (volumetric) within user’s range:
++ Ulay to be visualized within user range:
[2%, 98%] → [0.000000, 84.141731]
++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./…/QC/__tmp_chauf_aOV7ti8h37D/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./…/QC/__tmp_chauf_aOV7ti8h37D/tmp_olay.nii
++ For olay, the 50%ile value leads to
→ upper range value: 360.823853
++ Dimensions (xyzt): 236 172 192 1
++ (initial) Slice spacing ordered (x,y,z) is: 21 26 19
++ 3dmaskdump: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ 7793664 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 117 85 95
\n------------------- end of optionizing -------------------\n
– trying to start Xvfb :393
[1] 65206
Precompiled binary macos_10.12_local: Dec 5 2018 (Version AFNI_18.3.15 ‘Augustus’)

+++ Command Echo:
afni -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com SET_PBAR_ALL +99 1 red_monochrome -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 84.141731 -com SET_FUNC_RANGE 360.823853 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS MULTI -com OPEN_WINDOW sagittalimage opacity=6 mont=3x3:21 crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=6 mont=3x3:26 crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=6 mont=3x3:19 crop=0:0,0:0 -com SET_IJK 117 85 95 -com SAVE_PNG sagittalimage …/QC/t1w_qc_ref_in.sag blowup=2 -com SAVE_PNG coronalimage …/QC/t1w_qc_ref_in.cor blowup=2 -com SAVE_PNG axialimage …/QC/t1w_qc_ref_in.axi blowup=2 -com QUITT …/QC/__tmp_chauf_aOV7ti8h37D

Thanks go to JA Butman for many suggestions

Initializing: X11[The X.Org Foundation v 11804000].
*** can’t get X11 colormap entry for overlay color ###
*** can’t get X11 colormap entry for overlay color for
*** can’t get X11 colormap entry for overlay color underlay
*** can’t get X11 colormap entry for overlay color AFNI_GLOBAL_SESSION. Widgets… Input files:
session # 1 = QC/__tmp_chauf_aOV7ti8h37D/ ==> 2 datasets
dataset count = 2
Time series = 5 files read
Plugins = 0 libraries read
++ Writing one 1416x1032 image to filter ‘/usr/local/bin/pnmtopng -compression 9 > …/QC/t1w_qc_ref_in.sag.png’
++ Writing one 1152x1032 image to filter ‘/usr/local/bin/pnmtopng -compression 9 > …/QC/t1w_qc_ref_in.cor.png’
++ Writing one 1152x1416 image to filter ‘/usr/local/bin/pnmtopng -compression 9 > …/QC/t1w_qc_ref_in.axi.png’

AFNI QUITTs!
\n+* Removing temporary image directory ‘…/QC/__tmp_chauf_aOV7ti8h37D’.\n
[1] + Done Xvfb :393 -screen 0 1024x768x24
\n++ NOT removing temporary axialization working dir: ‘/Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w’\n

++ DONE! View the finished, axialized product:
/Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/t1w.nii.gz

ptaylor · December 18, 2018, 3:41pm

Hmm, OK, well, it says that it output PNGs, and doesn’t show an error there. Are you able to find them in this directory called “QC/”?:


++ Writing one 1416x1032 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../QC/t1w_qc_xlzd.sag.png'
++ Writing one 1152x1032 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../QC/t1w_qc_xlzd.cor.png'
++ Writing one 1152x1416 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../QC/t1w_qc_xlzd.axi.png'

and


++ Writing one 1416x1032 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../QC/t1w_qc_ref_in.sag.png'
++ Writing one 1152x1032 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../QC/t1w_qc_ref_in.cor.png'
++ Writing one 1152x1416 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../QC/t1w_qc_ref_in.axi.png'

–pt

charujing123 · December 20, 2018, 5:03am

year, it does!
Great
Thanks Paul.
rujing

no png after fat_proc_axialize_anat

I/O path, same as above; just need the “proc” dirs now

reference anatomical volumes to which we axialize

hi paul, i think the netpbm is already in my macos.

bash-3.2$ brew install netpbm Warning: netpbm 10.73.22 is already installed and up-to-date To reinstall 10.73.22, run brew reinstall netpbm

Here is the output in the command during running the

reference anatomical volumes to which we axialize

fat_proc_axialize_anat -inset $path_P_ss/anat_00/s005a1001.nii -prefix $path_P_ss/anat_01/t1w -mode_t1w -refset $ref_t2w -extra_al_wtmask $ref_t2w_wt -out_match_ref -extra_al_opts “-newgrid 1.0” "

bash-3.2$ brew install netpbm
Warning: netpbm 10.73.22 is already installed and up-to-date
To reinstall 10.73.22, run `brew reinstall netpbm`

fat_proc_axialize_anat
-inset $path_P_ss/anat_00/s005a1001.nii
-prefix $path_P_ss/anat_01/t1w
-mode_t1w
-refset $ref_t2w
-extra_al_wtmask $ref_t2w_wt
-out_match_ref -extra_al_opts “-newgrid 1.0”
"