Hi AFNI experts,
AFNI version info (afni -ver):
Precompiled binary linux_centos_7_64: Nov 22 2023 (Version AFNI_23.3.09 'Septimius Severus')
My script:
animal_warper \
-input /home/awong/Data/rawdata/bids/Monkey/MRI_TEST2/sub-Y9810009/ses-001/anat/sub-Y9810009_ses-001_run-001_T1w.nii.gz \
-input_abbrev T1W \
-base /home/awong/Templates/macaque/nmt/NMT_v2.0_sym/NMT_v2.0_sym/NMT_v2.0_sym_SS.nii.gz \
-base_abbrev NMT2 \
-atlas_followers /home/awong/Templates/macaque/nmt/NMT_v2.0_sym/NMT_v2.0_sym/CHARM_in_NMT_v2.0_sym.nii.gz \
/home/awong/Templates/macaque/nmt/NMT_v2.0_sym/NMT_v2.0_sym/D99_atlas_in_NMT_v2.0_sym.nii.gz \
-atlas_abbrevs CHARM D99 \
-seg_followers /home/awong/Templates/macaque/nmt/NMT_v2.0_sym/NMT_v2.0_sym/NMT_v2.0_sym_segmentation.nii.gz \
-seg_abbrevs SEG \
-skullstrip /home/awong/Templates/macaque/nmt/NMT_v2.0_sym/NMT_v2.0_sym/NMT_v2.0_sym_brainmask.nii.gz \
-dset_followers /home/awong/Data/rawdata/bids/Monkey/MRI_TEST2/sub-Y9810009/ses-001/anat/sub-Y9810009_ses-001_run-001_T2w.nii.gz \
-dset_abbrevs T2W \
-outdir /home/awong/Data/derivatives/afni-23.3.09/macaque/sub-Y9810009 \
-ok_to_exist
Outputs:
++ Start animal_warper, ver = 3.61
++ Prepare for running djunct_overlap_check (ver = 0.46)
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /home/awong/Data/derivatives/afni-23.3.09/macaque/sub-Y9810009/QC/__workdir_olap_3LRH8ejFoo2/olapch_0_cp_ulay.nii
++ Just copy olay, bc ulay will get regridded
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /home/awong/Data/derivatives/afni-23.3.09/macaque/sub-Y9810009/QC/__workdir_olap_3LRH8ejFoo2/olapch_1_cp_olay.nii
++ Quietly run: 3drefit -space NMT2 olapch_0_cp_ulay.nii++ olay_alpha has known value: No
++ My command:
chauffeur_afni -ulay olapch_0_cp_ulay.nii -pass -pass -olay olapch_1_cp_olay.nii -ulay_range 0% 98% -func_range_perc_nz 98 -cbar Reds_and_Blues -pbar_posonly -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -opacity 3 -zerocolor black -prefix img00 -montx 1 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean -pass -pass -pass -set_dicom_xyz 0 0 0++ Using AFNI ver : AFNI_23.3.09
++ chauffeur ver : 6.61------------------ start of optionizing ------------------
++ Found input file: olapch_0_cp_ulay.nii
++ Found input file: olapch_1_cp_olay.nii
++ Using blowup factor: 2
++ Using opacity: 3
++ Making temporary work directory to copy vis files: ./__tmp_chauf_slDFu6STeB3
++ 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, 218.000000]
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_slDFu6STeB3/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_slDFu6STeB3/tmp_olay.nii
++ For olay, the 98%ile value leads to
--> upper range value: 877.000000
++ Dimensions (xyzt): 320 320 192 1
++ (initial) Slice spacing ordered (x,y,z) is: 320 192 320
++ Will have user's chosen: SET_DICOM_XYZ 0 0 0------------------- end of optionizing -------------------
-- trying to start Xvfb :202
[1] 3335062+++ 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=3 mont=1x1:320:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=3 mont=1x1:192:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=3 mont=1x1:320:1:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 218.000000 -com SET_FUNC_RANGE 877.000000 -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 0 0 0 -com SAVE_JPEG axialimage ./img00.axi blowup=2 -com SAVE_JPEG sagittalimage ./img00.sag blowup=2 -com SAVE_JPEG coronalimage ./img00.cor blowup=2 -com QUITT ./__tmp_chauf_slDFu6STeB3+/home/awong/Data/derivatives/afni-23.3.09/macaque/sub-Y9810009/QC/__workdir_olap_3LRH8ejFoo2/__tmp_chauf_slDFu6STeB3++ Writing one 640x384 image to filter '/home/awong/Software/fsl/bin/cjpeg -quality 95 > ./img00.axi.jpg'
++ Writing one 384x640 image to filter '/home/awong/Software/fsl/bin/cjpeg -quality 95 > ./img00.sag.jpg'
++ Writing one 640x640 image to filter '/home/awong/Software/fsl/bin/cjpeg -quality 95 > ./img00.cor.jpg'AFNI QUITTs!
+* Removing temporary image directory './__tmp_chauf_slDFu6STeB3'.
[1] Done Xvfb :202 -screen 0 1024x768x24
++ DONE (good exit)
see: ./img00*+++ Arranging 3 images (each 640x384) into a 3x1 matrix.
+++ Transforming all input to rgb for a good reason
+++ Writing image to ../init_qc_00.input+base.T1W.jpg
You can view image ../init_qc_00.input+base.T1W.jpg with:
aiv ../init_qc_00.input+base.T1W.jpg+* Removing temporary workdir '/home/awong/Data/derivatives/afni-23.3.09/macaque/sub-Y9810009/QC/__workdir_olap_3LRH8ejFoo2*'
++ DONE! Image output:
/home/awong/Data/derivatives/afni-23.3.09/macaque/sub-Y9810009/QC/init_qc_00.input+base.T1W++ Using user's base abbrev: NMT2
++ 3dcopy: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ 3dcopy: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ 3dcopy: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ 3dcopy: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Using user-entered list of atlas_follower abbrevs
++ Using user-entered list of seg_follower abbrevs
++ Using user-entered list of dset_follower abbrevs
ans: Subscript out of range.
** ERROR: program failed (align centers)
The program was aborted. What's wrong with it? Do I need to do any prior manipulations to the input dataset?
Thanks,
Angel