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sotnir / NENAH-BIDS

A collaborate platform for streamlining a BIDS workflow for the NENAH study, on the linux workstation based at University of Southampton.
https://www.southampton.ac.uk/cndng
Creative Commons Zero v1.0 Universal
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FreeSurfer #17

Closed yukaizou2015 closed 2 years ago

yukaizou2015 commented 3 years ago

https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads

https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime

yukaizou2015 commented 3 years ago

Relocate to /local/scratch/software to free up space

Update bashrc_yz23e20:

export FREESURFER_HOME=/local/scratch/software/freesurfer/7.2.0-1
export FSFAST_HOME=/local/scratch/software/freesurfer/7.2.0-1/fsfast
export SUBJECTS_DIR=/local/scratch/disk2/research/freesurfer/subjects  # avoid utilising the /local space
export PATH=/local/scratch/software/freesurfer/7.2.0-1/bin:$PATH

Code that can get fMRIprep #69 running:

docker run -ti --rm \
    --volume $rawdatadir:/data:ro \
    --volume $FREESURFER_HOME/license.txt:/opt/freesurfer/license.txt \
    nipreps/fmriprep \
        /data \
        $studydir/derivatives/fmriprep \
        participant \
        --participant_label ${sID} \
    > $logdir/sub-${sID}_fmriprep_participant.log 2>&1
yukaizou2015 commented 2 years ago

Undefined variable $FREESURFER caused termination of recon-all by error. See here for details. This has been fixed in an updated version.

To work around, add export $FREESURFER=$FREESURFER_HOME to .bashrc One can resume recon-all using the autorecon2-fill flag.

yukaizou2015 commented 2 years ago

Running subfield/nuclei segmentation modules

Install Matlab Runtime for FS version 7 (see here):

fs_install_mcr R2014b

Experiencing space issue:

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archives/3p/cuda_glnxa64_1406353968.enc:  write error (disk full?).  Continue? (y/n/^C)

Then create a symbolic link named MCRv84 in the FreeSurfer directory that points to the main matlab install directory:

cd <FreeSurferRootDirectory> && ln -s <MatlabRootDirectory> MCRv84
yukaizou2015 commented 2 years ago

Matlab Runtime

For FS version 7, MCR 8.4 (R2014b) is needed.

fs_install_mcr R2014b

R2014b installed successfully in /local/scratch/software/freesurfer/7.2.0-1/MCRv84. Closing this ticket now.