[Freesurfer] Fixing talairach registration

After reading the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, I understand that I should be using "tkregister2 --mgz --s SUBJECT --fstal --surf orig" when editing my talairach transform. I have been somewhat successful at this, but I was wondering if there might

[Freesurfer] white matter edits

According to the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits, we should be looking for these holes in the white surface, but when I looked at my processed data using tkmedit SUBJECT brainmask.mgz -aux wm.mgz -surfs, I saw many such holes. They seem to be ub

[Freesurfer] memory and bus failure

I have three scans that exit with errors that I cannot comprehend. The first two indicate memory and bus failures, so I thought maybe my computer had choked during processing, but after running again I received the same errors. The third is too cryptic for me to understand at all. Can anyone

[Freesurfer] talairach.xfm

I am having trouble with 2 scans that exit with errors. Both have the same error: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** This is actually preceded by a message stating that talairach.xfm already exists and will not be copied. If I use the --clean-tal option

[Freesurfer] talairach_with_skull_2.lta missing

In article http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix, it is mentioned that talairach_with_skull_2.lta is created during autorecon2, and that it can be useful when troubleshooting skull-strips, however I do not find talairach_with_skull_2.lta in the mri/transforms director

[Freesurfer] Too many levels of symbolic links

I have subjects exiting with errors and I'm not sure why. The best clue I have is a line indicating "Too many levels of symbolic links" and an inability to read lh.BA1.label. Here are the last few lines of output: SUBJECTS_DIR/Applications/freesurfer/subjects FREESURFER_HOME /Applications/

[Freesurfer] Subcortical segmentation atlas

Hello, I am working on comparing hand-drawn subcortical volumes to those output automatically by FreeSurfer. While reading about the segmentation process on the wiki, I came across this line: "The final segmentation is based on both a subject-independent probabilistic atlas and subject-speci