[Freesurfer] A different question, pial problems near a temporal lesion

Dear FreeSurfer Development Team, An additional, but different question. One of my subjects has some sort of hole (lesion) in the left temporal lobe (slides 3-5). I have attached a powerpoint with screenshots in order to visualize the issue (

[Freesurfer] Problems with pial tracing near the insula

position? By the way, I am using the latest version of FreeSurfer (5.3.0) with a 3T Siemens TRIO. Thanks for your help. -Mark Fletcher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Correcting Pial Surfaces and adding control points at the same time?

run? Would it be something like this recon-all -autocron-pial -autorecon2-cp -autorecon3 -subjid randomsubject?? Thanks for your help in advance. -Mark Fletcher UIUC ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Edits to Pial and CP at the same time?

autorecon2*-cp-wm* -autorecon3 -subjid or recon-all -autorecon-pial *autorecon2-cp* *autorecon2-wm* -autorecon3 -subjid Thanks for your help :) Sincerely, Mark Fletcher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Using Subcortical initial output, with fixed cortical output

Dear FreeSurfers, I am using a Linux computer with FS 5.1 Due to the known feauture in version 5.1 where Control points may adversely affect aseg but also may alter the subcortical segmentation, is it acceptable to use the initial subcortical output (before adding control points) for analysis,

[Freesurfer] Changes to Sub-cortical Structures after adding WM control points

in version 5.1.0 mentioned in the release notes about running recon-all a second time? Please advise? Sincerely , Mark Fletcher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Changes to Sub-cortical Structures after adding WM control points

Do you know when the next version is slated to launch? That being said, if I wanted to salvage my work so far, is it best to just use the original subcortical output as is (if I was not trying to change it in the first place?). -Mark Fletcher On Wed, Oct 17, 2012 at 12:01 PM, Bruce Fischl fis

[Freesurfer] More problems created when adding WMCP

processing. Also, do you have any suggestions on how we might proceed? Is there a way besides adding WMCP to assist our fixing of the anterior temporal regions? Thanks in advance. Sincerely, Mark Fletcher ___ Freesurfer mailing list Freesurfer

[Freesurfer] Making Anatomical Mass for optical data

to get into either space). Thanks you so much for your help. Sincerely, Mark Fletcher CNL Lab UIUC ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail

[Freesurfer] Longitudinal Edits, skull strip and wmcp, how to do this longitudinally

For some of my subjects, I need to make many different types of edits on my longitudinal data, but have a few questions regarding the order/how to do this. I have read the details of this website ( http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) but wanted to confirm a few

[Freesurfer] Longitudinal Processing, can I salvage cross-sectional edits during processing stream? Mark

Dear Everyone, First of all, I have been very impressed by the functionality and abilities of FreeSurfer. I have a question about the longitudinal processing stream. I have two sets of MRI at two different time points for elderly individuals. Before version 5.1 came out, I ran the first years