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Hello.
I manually edited the brainmask.mgz file for three subjects. This was done to prevent the pial surface from extending into non-cortical areas, in particular the soft-tissue near the brain stem, and some cerebellar areas. Usually this type of editing (just removing voxels from brianmask.mgz) doesn't give me any trouble, and I use the command recon-all -make all -subjid <subject_id> -sd <subject_dir> to then rebuild the surfaces.
However, the tail of the log shows that the pipeline exited with errors, with a few commands near the end related to curvstats and jacobian_white failing. The new surfaces seem to look fine in freeview. The edits to brainmask were registered correctly, but I'm still concerned that the errors might affect an mri_glmfit analysis. This is true for all three subjects I edited, which seems odd, and I'm not sure what would be causing this.
Below is a pastebin showing the relevant errors. The rest of the pipeline seems to execute without errors. I could send entire log if necessary.
https://pastebin.com/b4JX04AThttps://pastebin.com/raw/b4JX04AT
Thanks,
- Eli
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