is it in $FREESURFER/bin ? If so, is that folder in your path?
On 10/27/2022 12:49 PM, Gillian Grennan wrote:
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Realized I sent this to the support list not back to you! But it says
"command not found" when I run 3dvolreg and 3dvolreg.afni
On Wed, Oct 26, 2022 at 7:24 AM Douglas N. Greve
<dgr...@mgh.harvard.edu> wrote:
What happens when your run 3dvolreg.afni by itself (no options)
from the command line?
On 10/25/2022 4:41 PM, Gillian Grennan wrote:
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Hello FreeSurfer Developers,
I downloaded *MailScanner has detected a possible fraud attempt
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onto my local drive and am attempting to run preprocessing
through FSFAST. I wasn't able to get access to the .tar.gz Darwin
file but downloaded Xquartz, Freesurfer, FSL, and Matlab
individually and was able to source Freesurfer using the
following commands:
export FREESURFER_HOME=/Applications/freesurfer/7.3.2
export
PROJECT_DIR=/Users/angelafang/Library/CloudStorage/OneDrive-UW/VicExt
export SUBJECTS_DIR=$PROJECT_DIR/subjects
source $FREESURFER_HOME/SetUpFreeSurfer.sh
However, when I run preproc-sess in my analysis folder I get the
following error:
command: preproc-sess -sf subjectlist -fsd bold -stc siemens
-surface fsaverage lhrh -mni305 -fwhm 5 -per-run
error message:
++ Initializing alignment base
Choleski factorization failure in startup_lsqfit
mri_startup_lsqfit: bad call to startup_lsqfit!
++ Starting final pass on 44 sub-bricks: 0
Fatal Signal 11 (SIGSEGV) received
mri_3dalign_one
3dvolreg main
Bottom of Debug Stack
** AFNI version = AFNI_2011_12_21_1014Compile date = May 22 2013
** [[Precompiled binary macosx_10.7_Intel_64: May 22 2013]]
** Program Abort **
** 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.
ERROR: 3dvolreg.afni
Invalid null command.
I'm confused on what more I need to install? Is there a way I can
get an updated link to the tar file with the relevant software
packages needed to run FSFAST?
Best,
Gillian Grennan
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