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 Freesurfer v7.3.2
<https://secure-web.cisco.com/1VuI2ndzXo5YBm-YeBraBeuWIVo2R7T-txZ30nSNYbmoPIkZ_3efq7PwRz6v6fLQ1pJlC62uAiZWEhoVn6TIP5AOC-fROlzfAXjpzBrhxOHTJD623bsr4Uy1g1CNJIrppL4ErFgccvgKfYMUKMpd1Mtd9LphNF1EzivYUbHHkO5us06GaXqFoIK58GT34oOb05UlLsCY5E80ZYb2YF4T_bzqK8EvCRd7mqezBcB5HNN58i32ZQ7Sv2U1pw14I7geTK0HBpESKhWXaMDpJFIFscIMo-OCdvDuTRDYPbzNlqEox4UsLm-KEODc30uQFKUqGrzBIaypcrdAH_0Mt2YFzSg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2F%2FFS7_mac>
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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