I am not sure what changed but QC was able to run, and AFNI opened! I do now receive the fatal signal 10 message when trying to run the next script in the pipeline though unfortunately (DWI_do_02.sh) .
Thanks Rick! We can correspond over email if this only pertains to me.
Kayla
Here is the output:
(base) ndsl-imab-2469:dwi-proc tognerikm$ ./DWI_do_02.sh p85
set: Variable name must begin with a letter.
++ Start imager script version: 2.32
++ My command:
@djunct_4d_imager -inset /Volumes/Shares/NEU/Data/sub-p85/ses-research/dwi/sub-p85_ses-research_acq-Siemens_dir-down_dwi.nii.gz -prefix /Volumes/Shares/NEU/Projects/DWI/p85/sel/qc_images/dwi_down
++ Found inset file: /Volumes/Shares/NEU/Data/sub-p85/ses-research/dwi/sub-p85_ses-research_acq-Siemens_dir-down_dwi.nii.gz
++ Making working directory: /Volumes/Shares/NEU/Projects/DWI/p85/sel/qc_images/__WORK_imgr_hkmLllQMrHV
\n-----> STARTING imager ---->
++ Iteration #1
++ Going to view slice [43]
+* WARNING: dset wasn't floats, but will be converted
to float for image-making purposes!
++ Command line: ['/Users/tognerikm/abin/adjunct_calc_mont_dims.py', '45', 'padcombo.dat']
++ OK, have my integer argument: 45
[1, 3, 5]
[45, 15, 9]
2 9 5 0.11246117974981074
++ OK! Good enough
---------------------------------------------
++ final Nslices = 45 (pad = 0)
++ -> Ncol x Nrow = 9 x 5
---------------------------------------------
++ Slicing...
++ from3d: AFNI version=AFNI_23.1.00 (Apr 7 2023) [64-bit]
++ Authored by: B. Douglas Ward
++ ...and gluing.
++ to3d: AFNI version=AFNI_23.1.00 (Apr 7 2023) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
++ Counting images: total=45 2D slices
++ Each 2D slice is 110 X 110 pixels
++ Image data type = float
++ Reading images: ......................
++ 3D dataset written to disk
++ 3drefit: AFNI version=AFNI_23.1.00 (Apr 7 2023) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset padcombo.nii
+ deoblique
+ loading and re-writing dataset padcombo.nii (/Volumes/Shares/NEU/Projects/DWI/p85/sel/qc_images/__WORK_imgr_hkmLllQMrHV/padcombo.nii in NIFTI storage)
++ 3drefit processed 1 datasets
set: Variable name must begin with a letter.
++ My command:
@chauffeur_afni -ulay padcombo.nii -prefix dwi_down_qc_onescl_1 -olay_off -montx 9 -monty 5 -ulay_range 1% 99.5% -label_mode 1 -label_size 4 -image_label_ijk
++ Using AFNI ver : AFNI_23.1.00
++ chauffeur ver : 6.52
\n------------------ start of optionizing ------------------\n
++ Found input file: padcombo.nii
++ Using blowup factor: 2
++ Using opacity: 6
++ Making temporary work directory to copy vis files: ./__tmp_chauf_opsHEYymTbw
++ 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:
[1%, 99.5%] -> [0.000000, 652.000000]
++ 3dcalc: AFNI version=AFNI_23.1.00 (Apr 7 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_opsHEYymTbw/tmp_ulay.nii
++ No overlay viewing
set: Variable name must begin with a letter.
++ Dimensions (xyzt): 110 110 45 1
++ (initial) Slice spacing ordered (x,y,z) is: 2 2 1
set: Variable name must begin with a letter.
set: Variable name must begin with a letter.
++ 3dmaskdump: AFNI version=AFNI_23.1.00 (Apr 7 2023) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=padcombo.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/g8w816m11w382s0kx795dtwnh1x3j0/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_lLljuw0Nb7ByBPfsHs3Qog argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_23.1.00 (Apr 7 2023) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.114350
++ Computing output statistics
++ Output dataset /var/folders/c0/g8w816m11w382s0kx795dtwnh1x3j0/T/3dcalc_AFN_lLljuw0Nb7ByBPfsHs3Qog+orig.BRIK
++ 544500 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 55 54 22
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :73
[1] 54244
+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_ulay.nii -com SEE_OVERLAY - -com OPEN_WINDOW sagittalimage opacity=6 mont=9x5:2:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=6 mont=9x5:2:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=6 mont=9x5:1:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 1 Plasma -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 652.000000 -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 OFF -com SET_XHAIR_GAP -1 -com SET_IJK 55 54 22 -com SAVE_PNG axialimage ./dwi_down_qc_onescl_1.axi blowup=2 -com SAVE_PNG sagittalimage ./dwi_down_qc_onescl_1.sag blowup=2 -com SAVE_PNG coronalimage ./dwi_down_qc_onescl_1.cor blowup=2 -com QUITT ./__tmp_chauf_opsHEYymTbw
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++ If you are using XQuartz 2.7.10 (or later), and AFNI crashes when
+ opening windows, or you cannot type text into AFNI popup windows,
+ you might need to set an environment variable to solve this problem:
+ setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace # tcsh
+ export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace # bash
+ This command is best put in your startup ~/.cshrc file, so that
+ it will be invoked for every (t)csh shell you open (mutatis mutandis
+ for the bash shell, of course).
+
+ If things are OK and you want to avoid having this warning message
+ pollute your terminal, use this:
+ setenv AFNI_SKIP_DYLD_WARNING YES # tcsh
+ export AFNI_SKIP_DYLD_WARNING=YES # bash
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Warning: Widget must be a VendorShell.
Fatal Signal 10 (SIGBUS) received
Last STATUS: creating top_form
AFNI_make_widgets
new_AFNI_controller
MAIN_workprocess
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_23.1.00 Compile date = Apr 7 2023
** [[Precompiled binary macos_10.12_local: Apr 7 2023]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /Users/tognerikm/.afni.crashlog
\n+* Removing temporary image directory './__tmp_chauf_opsHEYymTbw'.\n
[1] + Done Xvfb :73 -screen 0 1024x768x24
++ DONE (good exit)
see: ./dwi_down_qc_onescl_1*
