Re: [Freesurfer] Merging PArcellation labels

2013-03-24 Thread Christophe Destrieux
Hi did you look at : https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-June/014620.html cheers -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cer

Re: [Freesurfer] Freesurfer Digest, Vol 109, Issue 21

2013-03-24 Thread Rotem Saar
Hi Doug, Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ? When I first run the script, I got all values and looked the the CC - it looked

[Freesurfer] How to get transform matrix from Vertex Index to Vertex RAS

2013-03-24 Thread ZhiLiangLong
Hi all: I am studying the coordinate system transforms within subject across imaging modalities on web page: http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems. I met a problem. First, i run tksurfer : tksurfer subjectname lh inflated -reg register.dat -ov mov.nii , then i chose a p

[Freesurfer] How to transform a ROI volume to dwi space?

2013-03-24 Thread Ran Xu
Dear Freesurfer experts, I got the individual ROI volumes (not the surface) from aparc+aseg.nii.gz file, now I wanna use them as the seed regions in dwi space. I noticed that these ROIs are in the same space with "T1_brain", but this "T1_brain" is not the native T1. So could I register this T1_bra

Re: [Freesurfer] Brodmann area thickness, surface area and volume

2013-03-24 Thread _andreia_
Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the B

[Freesurfer] R: Re: R: Re: hippo subfield

2013-03-24 Thread stdp82
Hi Zeke, process finished without error in 2h. Thanks, Stefano Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 23-mar-2013 20.13 A: "freesurfer@nmr.mgh.harvard.edu" Ogg: Re: [Freesurfer] R: Re: hippo subfield It's not enough to simply put the zip file in the /Applications