AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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November 24, 2021 02:19AM
Greetings,

I have errors in running my preprocessing script by using uber_subject.py. Details are as follows

for i in 'cat subjList.txt'; do
> tcsh proc_mci.sh $i;
> mv ${i}.results $i;
> done
auto-generated by afni_proc.py, Tue Nov 23 12:40:47 2021
(version 7.17, July 16, 2021)
execution started: Wed Nov 24 11:31:18 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: 3dcopy needs input AND output filenames!
** Program compile date = Jul 28 2021
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/mci/sub-01/cat/func/cat_rest-MCI.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:
++ 3dTshift: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
** FATAL ERROR: Can't open input dataset 'pb00.cat.r01.tcat+orig'
** Program compile date = Jul 28 2021
++ 3dbucket: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
can't open dataset pb01.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/mci/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
Subject Author Posted

Afni preprocessing

Fizza November 24, 2021 02:19AM

Re: Afni preprocessing

ptaylor November 24, 2021 01:40PM