[Freesurfer] bbregister - Are 6 dof enough for MNI305?

within autorecon1 is a 12 dof affine, so I'm guessing that bbregister is unlikely to fully register the PET data to the template space in the same way that (eg) brain.mgz is registered. Thank you very much! Best, Joao Pereira ___ Freesurfer ma

[Freesurfer] PET analyses in cortical regions

bust (or correct...)? Also, does mri_segstats also give overall group statistics (mean, std) for each region, or must I use another function/average all subjects together for that? Thank you very much! Best, Joao Pereira Wolfson Brain Imaging Centre University of C

RE: [Freesurfer] Voxel resolution impact / skull stripping and biascorrection replacement

ira Junior Sent: 03 October 2008 21:25 To: Joao Pereira Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Voxel resolution impact / skull stripping and biascorrection replacement João, Here is my opinion: I have worked on resolutions distinct than 1mm3 isotropic and usually

[Freesurfer] Voxel resolution impact / skull stripping and bias correction replacement

ch for all your help! Best, Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Tksurfer rendering problem

permitted) libGL error: reverting to indirect rendering I'm using the freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.2 version. Any ideas as to what is going on? Thank you very much for your help. Best, Joao Pereira ___ Freesurfer mailing

[Freesurfer] Average subject for controls

ch with 20 subjects (controls+cohort1 and controls+cohort2). What would you say is the least biased/more robust approach? Thank you! Joao Pereira -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Bruce Fischl Sent: 15 August 2008 04:11 To: Nick Schmansky Cc:

[Freesurfer] TIV estimation with FreeSurfer

Dear all, I am posting the questions I made to Bruce without going through the list along with his reply. **I would still like to be sure about question 1)***, as it is central to my conclusions. If anyone has any other ideas, please let me know. >There are still a couple of questions in my mind

[Freesurfer] TIV estimation using FreeSurfer

ents. This affected talairach.xfm. Is this the adequate approach for TIV estimation purposes? I remember reading something about talairach_with_skull.lta... Thank you very much for your patience and assistance! Regards, Joao Pereira ___ Freesurfer ma

[Freesurfer] -notalairach error?

Hi, I have just realized I made a mistake when I ran recon-all -s subj -notalairach -autorecon1 -autorecon2, as the -notalairach option is overridden by autorecon1. Nevertheless, when I look at the dates of the files, I see that talairach.xfm is the one I edited, although talairach.log has a poste

[Freesurfer] Segmentation optimization

there any parameters to change in order to optimise the segmentation process? Also, in order to evaluate the segmentation I want to use the grey matter segmented volume mask. Is it the ?h.ribbon.mgz files or should I consider something else? Thank you again. Joao Pe

[Freesurfer] Cortical thickness difference measurement

what function did you use to subtract the subjects' average cortical thickness files in order to have a cortical thickness difference layer. I don't know if this is a very basic question, but I can't seem to find how to do it with FS. Thank you

[Freesurfer] Segmentation

noticed that the grey/white boundary in the original subjects was too conservative, hence no changes were detected (at least I believe it is the only explanantion). Is it possible to change the segmentation parameters to make it more "agressive" or am I overlooking something? Thank you! Jo

[Freesurfer] recon-all error

What is happening? Thanks! Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] aseg step bypass

procedures are affected. Is it OK to do this then? Thank you! Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] Skullstripping

Behalf Of Jenni Pacheco Sent: 28 April 2006 12:14 To: 'Joao Pereira'; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Skullstripping Which version of Freesurfer are you using? The newest versions write a file called brainmask.mgz, but the subsequent steps do recognize and use thi

[Freesurfer] Skullstripping

Can someone explain me why my the recon-all skull stripping option is writting a file named brainmask.mgz instead of brain.mgz? This is a problem because the subsequent procedures do not recognize the file. Thank you! JP ___ Freesurfer mailing list Fre

[Freesurfer] csurf porblem

lease help me qith this? Thank you, Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer