Errors after For Loop

AFNI Message Board
1

Greetings,

I am doing preprocessing using the script file and following all steps but after running for loop getting errors. Kindly help me to fix these fatal errors. Details are as follows:

for i in ‘cat subjList.txt’; do

tcsh proc_AD.sh $i;
mv ${i}.results $i;
done
auto-generated by afni_proc.py, Wed Sep 29 13:32:45 2021
(version 7.17, July 16, 2021)
execution started: Thu Nov 25 12:37:28 PKT 2021
Precompiled binary linux_ubuntu_16_64: Jul 28 2021 (Version AFNI_21.2.04 ‘Nerva’)
– is current: afni_history as new as: 27 Jun 2019
most recent entry is: 27 Jul 2021
++ 3dcopy: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
** FATAL ERROR: no datasets found!
** Program compile date = Jul 28 2021
++ 3dTcat: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
** FATAL ERROR: Can’t open dataset /mnt/d/MRIMS/84/AD/sub-01/func/sub-01_task-AD.nii
** Program compile date = Jul 28 2021
++ 3dToutcount: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
** Can’t open dataset pb00.cat.r01.tcat+orig
** ERROR: mri_read_ascii: can’t read any valid data from file outcount.r01.1D
** Can’t read time series file outcount.r01.1D{0}
++ 3dTstat: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: KR Hammett & RW Cox
** ERROR: mri_read_ascii: can’t read any valid data from file outcount_rall.1D
** Can’t read 1D dataset file outcount_rall.1D’
** FATAL ERROR: Can’t open dataset outcount_rall.1D’
** Program compile date = Jul 28 2021
min outlier: run out.pre_ss_warn.txt outcount.r01.1D outcount_rall.1D stimuli, TR error:
++ 3dDespike: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: RW Cox
** FATAL ERROR: Can’t open dataset ‘pb00.cat.r01.tcat+orig’
** Program compile date = Jul 28 2021
++ 3dTshift: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
** FATAL ERROR: Can’t open input dataset ‘pb01.cat.r01.despike+orig’
** Program compile date = Jul 28 2021
++ 3dbucket: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
can’t open dataset pb02.cat.rout.pre_ss_warn.txt
#++ align_epi_anat version: 1.62
#++ turning off volume registration
** ERROR: Could not find epi / dset2 dataset
/mnt/d/Fizza/84/ad/sub-01/cat.results/vr_base_min_outlier+orig
** ERROR - script failed
Error: Anatomical dset sub-01_T2_ns+orig not found.
** ERROR: THD_read_dvecmat: can’t open dataset sub-01_T2_ns+tlrc
** FATAL ERROR: Can’t read matrix from ‘sub-01_T2_ns+tlrc::WARP_DATA’
** Program compile date = Jul 28 2021
** missing +tlrc warp dataset: sub-01_T2_ns+tlrc.HEAD
mv: target ‘subjList.txt’ is not a directory

2

Hi-

This is another case where seeing the “afni_proc.py …” command will be useful/necessary to help.

My guess is that the input file paths or names are not correct in the afni_proc.py command. That is the first “ERROR …” message I see above. In particular, the script complains about not being able to find this file:


/mnt/d/MRIMS/84/AD/sub-01/func/sub-01_task-AD.nii

Can you check and see if that is really findable/correctly entered (and, for example, if the diskdrive hold it is really mounted at the time of running the command, since the path starts with “/mnt/…”. You can do this by copy+pasting:


ls -l /mnt/d/MRIMS/84/AD/sub-01/func/sub-01_task-AD.nii

in the terminal, for example, and seeing if that gives an error.

–pt