Hi,
I'm new to Freesurfer and am trying to process some data for the first time. I have two questions:
1. I have done some manual editing of the brainmask for skullstripping, saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing?
2. For then initial analysis of my data, I would like to create a table of intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line:
mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm
However, this fails with the error: unknown option --surf-ctxgmwm.
What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table.
Thank you for any assistance or suggestions.
Kind regards, Cheryl