[Freesurfer] Errors in WM surface persistent after manual edits to wm.mgz
External Email - Use Caution Dear Freesurfer Developers, Our study is implementing the longitudinal processing pipeline in FS 6.0. When attempting to make manual white matter edits to our subjects, the edits save but do not appear to impact the white matter surface. We are using the voxel-edit tool in freeview and recon-editing is selected, and the edits are made on the wm.mgz volume. Below are the commands we use to make and submit the edits... Command to open and edit WM: freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red Command to submit edits: recon-all -autorecon2-wm -autorecon3 -subjid Thank you in advance, Rachel Hoel Research Assistant Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Including a hyperintensity in wm surface
External Email - Use Caution Dear Freesurfer Developers, Our study is using the longitudinal processing pipeline with version 6.0. We have one subject where there is a hyperintenisty in the right temporal lobe, and even after adding several control points and running recon-all, the white matter is still not fully being included in the surface. The coordinates are about [83, 163, 139]. For this particular subject, we are performing both white and grey matter edits starting at the cross-sectional. I've tried adding multiple rounds of control points; and also removed all the control points and tried filling in wm voxels, but I can never get that region to be fully included. I uploaded the subject about a week ago and was hoping that someone could take a look. Best, Rachel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Right Lateral Ventricle Omitted from white and pial surfaces
External Email - Use Caution Thank you, I am still checking in with my supervisors about sending the subject. For now, if we are only interested in looking at grey matter data, do we need to be concerned if the subcortical segmentation isn’t accurate? Best, Rachel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Using freeview to view (and edit?) talairach registrations
External Email - Use Caution Dear Freesurfer Developers, I'm working with v6.0 on OS Catalina 10.15 and I'm trying to use freeview to check talairach registrations - I've always used tkmedit, so I am running into some issues with the command line for viewing the transform. When I run the following command: freeview -v /mri/T1.mgz \ /mri/brainmask.mgz:reg=/mri/transforms/talairach.xfm I get the following errors: regio_read_mincxfm: No such file or directory ERROR: could not read /mri/transforms/talairach.xfm ERROR: could not read /mri/transforms/talairach.xfm Thanks in advance! Rachel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
