Here is yet another update. What I did in order to fix the problem with the "libjpeg.9.dylib" file was the following.

- I found this file under my AFNI installation (/Applications/AFNI/abin).
- I then copy-pasted the file libjpeg.9.dylib to /usr/local/lib

This folder is one of the three folders where AFNI tried to search this file before, as you can see here

  Reason: tried: '/sw/lib/libjpeg.9.dylib' (no such file), '/usr/local/lib/libjpeg.9.dylib' (no such file), '/usr/lib/libjpeg.9.dylib' (no such file)

I then ran AFNI proc again and it worked (insofar as the problem with the libjpeg.9.dylib no longer appears). Here is my AFNI proc script first:

afni_proc.py \
-subj_id ${subject}_Rest \
-out_dir $directory/Results \
-dsets \
	$directory_warp/Warp_Align_Nwarp_RestingState_${subject}+tlrc \
-blocks despike tshift volreg mask blur regress \
-copy_anat $directory_warp/anat_final+tlrc \
-anat_has_skull no \
-tcat_remove_first_trs 4 \
-mask_segment_anat yes \
-mask_segment_erode yes \
-regress_anaticor \
-regress_ROI WMe CSFe \
-regress_apply_mot_types demean deriv \
-regress_motion_per_run \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.05 \
-blur_size 8.0 \
-regress_est_blur_epits \
-regress_est_blur_errts \
-html_review_style pythonic \
-execute

However, now another problem (and I am sure it is related to the problem stream inside my topic here) appears. After AFNI proc is done with preprocessing, it prints the following output (and QC images are also not produced):

subject ID                : Subject1_Rest
AFNI version              : AFNI_22.1.01
AFNI package              : macos_10.12_local
TR                        : 2.0
TRs removed (per run)     : UNKNOWN
num stim classes provided : 0
final anatomy dset        : anat_final.Subject1_Rest+tlrc.HEAD
final stats dset          : NO_STATS
final errts dset          : errts.Subject1_Rest.anaticor+tlrc.HEAD
final voxel resolution    : 3.000000	3.000000	3.000000

motion limit              : 0.3
num TRs above mot limit   : 0
average motion (per TR)   : 0.00957877
average censored motion   : 0.00957877
max motion displacement   : 0.0697734
max censored displacement : 0.0697734
outlier limit             : 0.05
average outlier frac (TR) : 0.00101504
num TRs above out limit   : 0

num runs found            : 1
num TRs per run           : 236
num TRs per run (applied) : 236
num TRs per run (censored): 0
fraction censored per run : 0
TRs total (uncensored)    : 236
TRs total                 : 236
degrees of freedom used   : 19
degrees of freedom left   : 217

TRs censored              : 0
censor fraction           : 0.000000
num regs of interest      : 0

TSNR average              : 247.085
global correlation (GCOR) : 0.0126185
anat/EPI mask Dice coef   : 0.814849
blur estimates (ACF)      : 0.941663 6.66755 3.5636
blur estimates (FWHM)     : 0 0 0


apqc_make_tcsh.py -review_style pythonic -subj_dir . -uvar_json out.ss_review_uvars.json
++ Found 33 files for QCing.
Traceback (most recent call last):
  File "/applications/AFNI/abin/apqc_make_tcsh.py", line 652, in <module>
    tspace    = lat.get_space_from_dset(ap_ssdict['template'])
  File "/Applications/AFNI/abin/afnipy/lib_apqc_tcsh.py", line 329, in get_space_from_dset
    dset_fullpath = com.so[0]
IndexError: list index out of range

What would be your idea? Is this problem related to the problems that I faced before? Or do I deal with something else here? In case this problem is related to something else, then of course lets try to fix the previous problems first. Please let me know what you think is going on with my AFNI installation.

PS: after my last updates, the new output of

# A:
\ls -l /usr/local/bin/python3
# B:
\ls -l /usr/local/bin/python

is

lrwxr-xr-x  1 root  wheel  70 Apr  3 19:44 /usr/local/bin/python3 -> ../../../Library/Frameworks/Python.framework/Versions/3.10/bin/python3
lrwxr-xr-x  1 root  wheel  22 Apr  5 09:01 /usr/local/bin/python -> /usr/local/bin/python3

Thanks,
Philipp



Edited 2 time(s). Last edit at 04/05/2022 08:07AM by Philipp.