Re: [Freesurfer] fixing hemisphere leakage

Try fixing the aseg and running from there forward On Dec 28, 2011, at 9:05 PM, David Groppe wrote: > Thanks for the speedy response Bruce. > I'm running: > $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ > > -David > > On Wed, Dec 28, 2011 at 7:44 PM, Bruce Fischl > wrote: >> H

Re: [Freesurfer] fixing hemisphere leakage

Thanks for the speedy response Bruce. I'm running: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ -David On Wed, Dec 28, 2011 at 7:44 PM, Bruce Fischl wrote: > Hi David > > what version are you running? > > Bruce > > On Wed, 28 Dec 2011, David Groppe wrote: > >> Hi FreeSurfers, >>  

Re: [Freesurfer] fixing hemisphere leakage

Hi David what version are you running? Bruce On Wed, 28 Dec 2011, David Groppe wrote: > Hi FreeSurfers, > I'm trying to fix FreeSurfer's pial and white matter surface > boundary estimates on a brain missing a large part of the right > hemisphere. I've manually filled in the greatly expanded v

[Freesurfer] How to export non spatial normalization fMRI images?

Hi, I have run preproc-sess to analyze fMRI images. I'd like to analyze fMRI images in the individual space, but I found that the final output (i.e., fmcpr.up.sm4.fsaverage.lh.nii.gz) were already spatial normalized. So, How to just smooth fMRI images in surface space and export them as the co-regi

Re: [Freesurfer] Setting Up Source File Automatically

The log off/on fixed it. Thanks. Brian. -Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: December-28-11 3:28 PM To: James, Brian Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Setting Up Source File Automatically when you changed your shel

Re: [Freesurfer] Setting Up Source File Automatically

when you changed your shell, did you run: chsh -s `which tcsh` ? usually it will prompt for your password. then you will need to logout/login. when you type 'ps', you should see 'tcsh' as one of the processes. also, you can try copying the .tcshrc to .cshrc, but probably that shouldn't mat

Re: [Freesurfer] recon-all problem

what does the file transforms/talairach_avi.log say? and are those pathnames real? or something the email added? n. On Wed, 2011-12-28 at 17:08 +, LAOUCHEDI MAKHLOUF wrote: > > Hi everyone > > I run freesurfer recon-all command with the flag -all and I have this > error > > > ERROR:mpr

Re: [Freesurfer] error with cvs registration

Dear Lilla, I solved the problem with my registration so now is working well but I will be very grateful if you can help me with the following questions: For the DTI group analysis study  I am interested to see any changes in the FA values within two groups: controls versus patients (children

[Freesurfer] Setting Up Source File Automatically

Hi - I am trying to setup the FreeSurfer program so that when I open the terminal it sources the file automatically. As per the instructions, I have changed my .tcshrc file in my Home Directory so that both the setenv and source commands are in there. I have also permanently changed my shell t

[Freesurfer] recon-all problem

Hi everyone I run freesurfer recon-all command with the flag -all and I have this error ERROR:mpr2mni305 failed, see transforms/talairach_avi.log Some one have any idea? Thanks  this is the whole process: Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK

[Freesurfer] wm edit freeview

Dear all, Is there any documentation on doing em edit using freeview. Thanks, SK ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for