[Freesurfer] Thickness histogram on labelled region only

I would like to look at the histogram of cortical thickness for the cingulate cortex because I am concerned that the edges next to the corpus callosum have very low thicknesses (and significant regions that are zero) that may be creating some interesting cingulate results we are seeing. I see ther

[Freesurfer] Thickness histogram on labeled region only?

I sent this a while back, but haven't received any suggestions. Would anyone have any ideas or suggestions? I would like to look at the histogram of cortical thickness for the cingulate cortex because I am concerned that the edges next to the corpus callosum have very low thicknesses (and signifi

[Freesurfer] Labeling surface to get thickness from a region

I am following up on some issues where we see some effects we really don't expect when analyzing our data with qdec. They look like they could be some slightly bad data from scan issues, segmentation problems, etc. This is a large set of scans so I would like to script out a routine to get the th

[Freesurfer] Using a clipped image

We have a large number of scans with excellent, visually inspected and manually trimmed brain masks, so we would like to use these masks to assist the FreeSurfer processing. One way we have experimented with to achieve this is to clip the T1 to remove anything non-brain before importing it into th

Re: [Freesurfer] Using a clipped image

Thanks! Yes, that makes perfect sense - looking at: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable Ron -Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: Thursday, January 28, 2010 3:04 PM To: Bruce Fischl Cc: Pierson, Ronald K; freesurfer

[Freesurfer] Longitudinal processing edits

I apologize if this has been covered before, but I wanted to make sure I understand the best way to edit at the appropriate times during the longitudinal stream. 1) Run recon-all -all on each scan 2) If needed, control points are chosen on the individual scans, and recon-all using

[Freesurfer] Editing annotations

Forgive me if this has been covered before, but I was unable to find an answer after searching for a bit. I have been considering editing the final surface parcellation for those scans that have problems in certain areas. Can these corrections then be used to correct the surface registration f

[Freesurfer] Combining two regions

I apologize if this has been asked and answered before, but I wish to combine rostral and caudal middle frontal gyri for a summary measure. To find the average thickness of the entire region, will it be weighted by the surface area or by the number of vertices? Avg_MidFront = ((CaudThick*NumVert