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:

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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