Re: [Freesurfer] Converting single voxel to surface space

you could just draw dots in the middle of the activated region I guess On Thu, 10 Sep 2009 benjamin.d...@yale.edu wrote: > > Hi, > > The surface I got from MNI152 looks pretty good. > > I had tried to do what you're describing--I made 3x3x3 voxel cubes around > each > peak coordinate in the volu

Re: [Freesurfer] longitudinal processing QA, and problem with aparc+aseg

Hi Ryan, is this only in the longitudinal stream? Sounds like a bug. If you upload the whole subject directory we'll take a look. Bruce On Thu, 10 Sep 2009 muet0...@umn.edu wrote: > Hello, > > I am running the longitudinal processing using version 4.5 and was > wondering if there are any data

Re: [Freesurfer] multimodel wm hypointensity labeling?

Hi Tori, we have some prototype tools for this, but haven't gotten to the point of being able to distribute them. Koen Van Leemput (ccd) also has some very nice tools for this I believe. cheers Bruce On Thu, 10 Sep 2009, Victoria Williams wrote: > Hello, > > Are there any freesurfer tools t

[Freesurfer] Correlating two surfaces

Dear All, I would like to correlate two surfaces with glmfit e.g. thickness and curvature but I don't seem to be able to find any document explaining how to do that. Could you please point me in the right direction? Thanks Nic ___ Fre

[Freesurfer] Fwd: About the workflow of cortical thickness measurement.

-- Forwarded message -- From: QQ Liu Date: 2009/9/10 Subject: About the workflow of cortical thickness measurement. To: fis...@nmr.mgh.harvard.edu Hi Bruce, I want to do the cortical thickness measurement and I'm not sure the workflow in FreeSurfer commands in detail, becau

Re: [Freesurfer] editing aseg.mgz?

Does it look that way on the aparc+aseg.mgz? Kim, Miyoung wrote: > Hi. > > I wasn't sure if my previous email (below) went through - essentially we have > a cortical occipital area that Freesurfer, upon segmentation, labels it as > cerebellum even though the pial surface appears to have been out

Re: [Freesurfer] Surface area of ROI

If you pass 'mris_curvature_stats' a '-l ' it will output, amongst other, the surface area of the ROI, e.g.: $>mris_curvature_stats -l rh curv (will calculate a bunch of stats on the rh.curv file of -- just ignore and look for:) ... ... ROI Surface Area: ... ... -=R Barnali Basu wrote

[Freesurfer] Surface area of ROI

Experts, I have labels drawn on surfaces of individual subjects. I need to find the surface area of each (one on each surface). Is there a way I could do it? Thanks -- Barnali Basu Cell : 425 638 2936 Home: 206 257 0174 ___ Freesurfer mailing list

[Freesurfer] longitudinal processing QA, and problem with aparc+aseg

Hello, I am running the longitudinal processing using version 4.5 and was wondering if there are any data quality checks specific to the longitudinal stream (other than the standard ones listed for the cross-sectional analysis)? For example, is there a way to check the registration between TP1

[Freesurfer] multimodel wm hypointensity labeling?

Hello, Are there any freesurfer tools that allow labeling of wm hypointensities using imput from both T1 and T2 or lowb images? Also, I was wondering if there was further documentation for the use of the mri_relabel_hypointensities command? I got the impression this script dealt somehow with c

Re: [Freesurfer] qdec permission denied

Try changing the SELINUX setting from "enforcing" to "disabled" in the files '/etc/selinux/config' and/or /etc/sysconfig/selinux and reboot. Or try running '/usr/sbin/setenforce 0' as root. Nick On Thu, 2009-09-10 at 11:02 +0200, Ahmed, F, Me wrote: > Nick, > > I tried that command, and this h

Re: [Freesurfer] mris_volmask description

Hi Zeng, Here's the wiki for mris_volmask. https://surfer.nmr.mgh.harvard.edu/fswiki/mris%25volmask You can also find a description of it in the terminal window when you type in 'mris_volmask --help' or just mris_volmask. Sita. On Thu, 10 Sep 2009, Guang Zeng wrote: > > Hello, there, > >

[Freesurfer] Missing Volume Values

Hi Freesurfer team, Thank you in advance for your help. We are attempting to obtain left hemisphere and right hemisphere volumes for various grey and white matter structures in a variety of controls and brain injured patients. However, values for the corpus callosum are often not reported in

[Freesurfer] mris_volmask description

Hello, there, Do you know where I can find a description for mris_volmask. The page on FreeSurferWiki about this is empty. Thanks a lot! Zeng _ Windows Live: Make it easier for your friends to see what you’re up to on Facebook.

[Freesurfer] Post-surgery images

Hello! I would like to know if someone has experience with segmentation of post-operative images using freesurfer. Thanks! Paula -- == Paula Rejane Beserra Diniz Bacharel em Informática Biomédica Mestre em Neurociências Doutoranda em Neurociências Universidade de

Re: [Freesurfer] qdec permission denied

Nick, I tried that command, and this happened: [...@localhost freesurfer]$ /usr/sbin/setenforce 0 /usr/sbin/setenforce: setenforce() failed Am I missing something? -Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: 08 September 2009 19:01 To: Ahmed, F,