There is a bug in recon-all when trying to only run with one hemi
(actually there are several bugs). Currently, it is failing at
mris_volmask, which needs to have --lh appended to the command line. You
can do this with an expert options file. This is simple text file that
should have the contents
mris_volmask --lh
Also, when you run recon-all with -lh instead of -hemi lh
I think there will be more problems, but this might get an
aparc+aseg.mgz with only one hemi
On 8/30/20 6:32 AM, Alina Rojas wrote:
External Email - Use Caution
Hello Freesurfer experts,
i’m attempting to run recon-all on only one hemisphere for further
processing steps. For these I need wmparc.mgz, aparc.a2009s+aseg.mgz,
aparc+aseg.mgz.
recon-all -sd ${TARGET_FOLDER}-subjid $SUBJECTID-i $T1-qcache -openmp
${OMP_NUM_THREADS}-all -hemi lh -no-isrunning
It crashes before the files are made. How can I get these files? I
attached the recon-all.log file.
Thank you,
Alina Rojas
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