Pre processing errors using

Hello Everyone,

I am getting these errors while doing preprocessing in AFNI, Can anyone help to fix these.

for i in ‘cat subjList.txt’; do

tcsh $i;
mv ${i}.results $i;
auto-generated by, Wed Nov 24 16:26:38 2021
(version 7.17, July 16, 2021)
execution started: Thu Nov 25 10:41:58 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
Usage 1: 3dcopy [-verb] [-denote] old_prefix new_prefix ~1~
Will copy all datasets using the old_prefix to use the new_prefix;

3dcopy fred ethel

will copy fred+orig.HEAD to ethel+orig.HEAD
fred+orig.BRIK to ethel+orig.BRIK
fred+tlrc.HEAD to ethel+tlrc.HEAD
fred+tlrc.BRIK.gz to ethel+tlrc.BRIK.gz

Usage 2: 3dcopy old_prefix+view new_prefix ~1~
Will copy only the dataset with the given view (orig, acpc, tlrc).

Usage 3: 3dcopy old_dataset new_prefix ~1~
Will copy the non-AFNI formatted dataset (e.g., MINC, ANALYZE, CTF)
to the AFNI formatted dataset with the given new prefix.

Notes: ~1~

  • This is to copy entire datasets, possibly with multiple views.
    So sub-brick selection is not allowed. Please use 3dbucket or
    3dTcat for that purpose.

  • The new datasets have new ID codes. If you are renaming
    multiple datasets (as in Usage 1), then if the old +orig
    dataset is the warp parent of the old +acpc and/or +tlrc
    datasets, then the new +orig dataset will be the warp
    parent of the new +acpc and +tlrc datasets. If any other
    datasets point to the old datasets as anat or warp parents,
    they will still point to the old datasets, not these new ones.

  • The BRIK files are copied if they exist, keeping the compression
    suffix unchanged (if any).

  • The old_prefix may have a directory name attached in front,
    as in ‘gerard/manley/hopkins’.

  • If the new_prefix does not have a directory name attached
    (i.e., does NOT look like ‘homer/simpson’), then the new
    datasets will be written in the current directory (‘./’).

  • The new can JUST be a directory now (like the Unix
    utility ‘cp’); in this case the output has the same prefix
    as the input.

  • The ‘-verb’ option will print progress reports; otherwise, the
    program operates silently (unless an error is detected).

  • The ‘-denote’ option will remove any Notes from the file.

++ Compile date = Jul 28 2021 {AFNI_21.2.04:linux_ubuntu_16_64}

/mnt/d/Fizza/84/emci/sub-01/cat/anat/cat_T2.nii: Command not found.
cat.results/cat_T2: Command not found.
++ 3dTcat: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
** FATAL ERROR: Can’t open dataset /mnt/d/Fizza/84/emci/sub-01/cat/func/cat_rest-EMCI.nii
** Program compile date = Jul 28 2021
++ 3dToutcount: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
** Can’t open dataset
** 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:
++ 3dTshift: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
** FATAL ERROR: Can’t open input dataset ‘’
** Program compile date = Jul 28 2021
++ 3dbucket: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
can’t open dataset
#++ align_epi_anat version: 1.62
#++ turning off volume registration
** ERROR: Could not find epi / dset2 dataset
** 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


For some reason, the help of the 3dcopy command is being shown here—rather than executing the command itself.

I don’t often see that in the command. Has the script file that is being executed here been edited, for example (e.g., a backslash might be missing now)?