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Preproc worked -- it seems it was an issue in setting up my freesurfer set up file!
I am now running into an error with FSFAST functions that require MATLAB.
I downloaded MATLAB runtime using the command in freesurfer (fs_install_mcr R2014b) which downloaded the MCRv84 folder in my $FreesurferHome directory.
When running mkcontrast, it gives an error that it can't find Matlab. How would I go about adding this MCRv84 to my path?
I have seen suggestions to add variables to my startup.m file in the FreesurferHome/matlab folder but there is no startup.m file included there.
Thanks for your help!
On Tue, Nov 8, 2022 at 6:10 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
is it in $FREESURFER/bin ? If so, is that folder in your path?
On 10/27/2022 12:49 PM, Gillian Grennan wrote:
External Email - Use CautionRealized I sent this to the support list not back to you! But it says "command not found" when I run 3dvolreg and 3dvolreg.afni
On Wed, Oct 26, 2022 at 7:24 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
What happens when your run 3dvolreg.afni by itself (no options) from the command line?
On 10/25/2022 4:41 PM, Gillian Grennan wrote:
External Email - Use CautionHello FreeSurfer Developers,
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export FREESURFER_HOME=/Applications/freesurfer/7.3.2
export PROJECT_DIR=/Users/angelafang/Library/CloudStorage/OneDrive-UW/VicExt
export SUBJECTS_DIR=$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_1014 Compile 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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