See also Setting up and running FreeSurfer from CSPM and Display Problems.
Create a nifti file from FreeSurfer format
In Linux, open a terminal window, go to the directory where the file is stored, and use mri_convert; this will create a copy of the file in the new format (format is determined by extension).
Example - creating a nifti brain mask file for subject CCHS2002:
[...]$ cd /mnt/hgfs/LinuxShare/subjects/CCHS2002/mri
[...]$ mri_convert brainmask.mgz brainmask.nii
Correcting Pial Surface Errors from FreeSurfer
Correcting Pial Surface Errors from FreeSurfer.doc
Load subject with command: tkmedit subject_name brainmask.mgz rh.white -aux-surface lh.white
This will load TkMedit Tool box and the subject's brainmask.mgz in the coronal view.
- View screen can be adjusted to include 4 panels showing the coronal, saggital, and axial views. Although corrections will be made in the coronal, the saggital view will help clarify pial surface boundaries
- Access the Brush Info pane through Tools -> Configure Brush Info...
- Set configurations for brush shape and radius, circle usually works best for rounded surfaces although radius will have to be adjusted often according to region of interest.
- Remove non-brain areas that cause mistakes using the right mouse button.
- Before saving edits, backup main volume from subject directory
- Use command recon-all to re-run analysis. recon-all will save any edits previously made to brainmask.mgz as part of the new brainmask.mgz. The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. In order to overwrite brainmask.mgz, add the -clean-bm flag to recon-all. Refer to this website to troubleshoot reconstruction process: [link]
- When making general edits to pial surfaces refer to this section: [link] and when specifically making edits to correct for pial surface extensions into cerebellum refer to this section: [link]
Frequently Encountered Errors
1) Posterior Pial and Dural Boundaries (edits made in coronal panel)
2) Superior Frontal Pial and Dural/Skull Boundaries (edits made in coronal panel)
3) Inferior Frontal and Anterior Temporal Pial and Subdural boundaries (edits made in coronal panel)