[Freesurfer] Multiple flat surfaces

Hi, Is there a way to visualize multiple flat surfaces from the same brain in a single tksurfer window ? Thanks in advance. shriks Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/__

[Freesurfer] subcortical segmentation

Hi I have done the three recon-all steps of cortical segmentation in my data and I corrected manually the segmentation errors. Now, I will check the subcortical structures. The correction of this subcortical segmentation will afect the previous cortical segmentation? Thanks Abel _

Re: [Freesurfer] Multiple flat surfaces

I don't think so, sorry. YOu can always have multiple tksufers running of course. Bruce On Wed, 17 Sep 2008, SHRIKANTH KULASHEKHAR wrote: Hi, Is there a way to visualize multiple flat surfaces from the same brain in a single tksurfer window ? Thanks in advance. shriks Unlimited freed

Re: [Freesurfer] subcortical segmentation

mostly changing gray matter structures won't except in places like lateral putamen which can be so close to insula. The white matter in the aseg is used as the basis of the cortical intensity normalization, so if you change that substantially it will change the cortical estimates as well. Bruc

Re: [Freesurfer] Multiple flat surfaces

Hi Bruce , In that case would it be possible to flatten one whole hemisphere in freesurfer ? what is the best possible way to do this ? Thanks. shriks Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/_

Re: [Freesurfer] Multiple flat surfaces

yes of course. We do this all the time with the pattern of cuts shown in the 1999 surface-based analysis II paper. cheers, Bruce On Wed, 17 Sep 2008, SHRIKANTH KULASHEKHAR wrote: Hi Bruce , In that case would it be possible to flatten one whole hemisphere in freesurfer ? what is the best p

RE: [Freesurfer] freesurfer

Hi Bruce, Thanks for the advice. It works well. I was wondering if there's any way I could check what values of the label correspond to a particular brain region. Thanks. Cheers, HL -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl Sent: 16

RE: [Freesurfer] freesurfer

they are listed in $FREESURFER_HOME/FreeSurferColorLUT.txt cheers, Bruce On Wed, 17 Sep 2008, Hwee Ling Lee wrote: Hi Bruce, Thanks for the advice. It works well. I was wondering if there's any way I could check what values of the label correspond to a particular brain region. Thanks. Chee

RE: [Freesurfer] freesurfer

Hi Bruce, I was able to write the gyrus from the labels, however, when I tried to write one of the sulcus (1180), there was nothing in the image. Would I have to use a different input volume? Currently, I'm using aparc+aseg.mgz. Thanks, HweeLing -Original Message- From: [EMAIL PROTECTE

[Freesurfer] mri_convert and image orientation; Analyze format

Hello Freesurfers, Lately I've been scratching my head about image orientation problems. What I do here is take the DICOM images and use mri_convert to convert them into SPM Analyze format. The command I use is: mri_convert.x86_64.dev -dicomread2 "$experiment" --nskip ${nskip} \

[Freesurfer] mri_preproc

Hello When I run the mri_preproc command I am getting the message ERROR: cannot find fsaverage in /space/barlab_002/users/cibu/dep_LGI But the fsaverage folder is in the path and subjects_dir is set correctly. So I am not sure what's wrong with the command Here's the command I am trying to run mr