Thanks so much for your continued help with this. For each script, 3 image files are output (axial, coronal, sagittal) of a 3x3 slice montage without colorbars. The log files look nearly identical for both. I have copied the content for each below. One thing I noticed when looking at my afni_system_check is that although I am running Python 3.8 set up through Miniconda, it looks like the Python binaries are listed as Python 3.6. Would this be an issue? (see below)
python3 : 2
/Users/michaelspilka/miniconda3/envs/py38_afni_tiny/bin/python3.8
/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6
++ module loaded: matplotlib.pyplot
module file : /Users/michaelspilka/miniconda3/envs/py38_afni_tiny/lib/python3.8/site-packages/matplotlib/pyplot.py
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)
/usr/local/bin/python3.6 (sym link to /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)
Output for @chauffeur_afni scripts:
1:
++ My command:
@chauffeur_afni -ulay FT_anat+orig.HEAD -olay FT_anat+orig.HEAD -ulay_range_nz 0 1300 -func_range 1300 -box_focus_slices AMASK_FOCUS_ULAY -cbar gray_scale -pbar_posonly -pbar_saveim TEST1.pbar.jpg -pbar_comm_range test1 text -pbar_for dset -prefix TEST1 -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
\n------------------ start of optionizing ------------------\n
++ Found input file: FT_anat+orig.HEAD
++ Found input file: FT_anat+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ./__tmp_chauf_X1vYw23kNow
++ 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%, 98%] -> [0.000000, 1367.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_X1vYw23kNow/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_X1vYw23kNow/tmp_olay.nii
++ User-entered function range value value (1300)
++ Dimensions (xyzt): 256 256 175 1
++ (initial) Slice spacing ordered (x,y,z) is: 19 28 28
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=FT_anat+orig.HEAD[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN__NIEBKAc_v6IeDbIB2yG8g argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 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 = 0.062029
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN__NIEBKAc_v6IeDbIB2yG8g+orig.BRIK
++ 11468800 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 128 127 86
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :12
[1] 84203
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT/__tmp_chauf_X1vYw23kNow[7m*+ WARNING:[0m Bad drive AFNI result from 'SET_PBAR_ALL +99 -do_clean gray_scale'
++ Writing one 3072x3072 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./TEST1.sag.png'
++ Writing one 2240x3072 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./TEST1.cor.png'
++ Writing one 2240x3072 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./TEST1.axi.png'
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=3x3:19:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:28:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:28:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 -do_clean gray_scale -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 1367.000000 -com SET_FUNC_RANGE 1300 -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_IJK 128 127 86 -com SAVE_PNG sagittalimage ./TEST1.sag blowup=4 -com SAVE_PNG coronalimage ./TEST1.cor blowup=4 -com SAVE_PNG axialimage ./TEST1.axi blowup=4 -com QUITT ./__tmp_chauf_X1vYw23kNow
\n+* Removing temporary image directory './__tmp_chauf_X1vYw23kNow'.\n
++ DONE (good exit)
see: ./TEST1*
2:
++ My command:
@chauffeur_afni -ulay FT_anat+orig.HEAD -olay FT_anat+orig.HEAD -ulay_range_nz 0 1300 -func_range 1300 -box_focus_slices AMASK_FOCUS_ULAY -cbar gray_scale -pbar_posonly -pbar_comm_range test2 text -pbar_for dset -prefix TEST2 -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
\n------------------ start of optionizing ------------------\n
++ Found input file: FT_anat+orig.HEAD
++ Found input file: FT_anat+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ./__tmp_chauf_wQMY7brYUQG
++ 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%, 98%] -> [0.000000, 1367.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_wQMY7brYUQG/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_wQMY7brYUQG/tmp_olay.nii
++ User-entered function range value value (1300)
++ Dimensions (xyzt): 256 256 175 1
++ (initial) Slice spacing ordered (x,y,z) is: 19 28 28
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=FT_anat+orig.HEAD[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_PLAZKjh37xw2Cm9b8xKCLg argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 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 = 0.062029
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_PLAZKjh37xw2Cm9b8xKCLg+orig.BRIK
++ 11468800 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 128 127 86
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :157
[1] 84387
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT/__tmp_chauf_wQMY7brYUQG[7m*+ WARNING:[0m Bad drive AFNI result from 'SET_PBAR_ALL +99 -do_clean gray_scale'
++ Writing one 3072x3072 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./TEST2.sag.png'
++ Writing one 2240x3072 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./TEST2.cor.png'
++ Writing one 2240x3072 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./TEST2.axi.png'
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=3x3:19:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:28:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:28:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 -do_clean gray_scale -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 1367.000000 -com SET_FUNC_RANGE 1300 -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_IJK 128 127 86 -com SAVE_PNG sagittalimage ./TEST2.sag blowup=4 -com SAVE_PNG coronalimage ./TEST2.cor blowup=4 -com SAVE_PNG axialimage ./TEST2.axi blowup=4 -com QUITT ./__tmp_chauf_wQMY7brYUQG
\n+* Removing temporary image directory './__tmp_chauf_wQMY7brYUQG'.\n
++ DONE (good exit)
see: ./TEST2*
