[Freesurfer] mgz files not being recreated following recon-all

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Hello,

After running recon-all, and attempting to run freesurfer (using the command "checksurfswmflair") the following error message appears for number of studies:

Failed to load MRI /Volumes/MSdata/SAG_3D_BRAVO/MS2030181102/lesion/flair_on_T1.flirt.nii.gz

It seems that gz lesion files are not being created/carried-over for these studies after being run through my script (other studies interestingly are opening up successfully using the same script). The successful studies seem to contain the zip file.

Any thoughts as to why certain studies which contain nii.gz files are failing to recompress after being processed?

Thanks,

Charlie