Re: [Freesurfer] VM ubuntu developer password

External Email - Use Caution I have also just ran into this issue. Can someone send me the password as well? Thansk, Cyrus Cyrus Sarosh [1587656965587] Research Area Specialist Intermediate Department of Radiology Functional Neuroimaging, Cognitive and Mobility Laboratory Domi

[Freesurfer] Moving VOI to FreeSurfer Space

External Email - Use Caution Hello FreeSurfer Experts, I'm trying to find the best method and command to move a hand drawn VOI in original MRI space to FreeSurfer space. These scans have already been ran through the entire FreeSurfer process and the hand drawn VOIs have already

[Freesurfer] Cerebellar Vermis

We are interested in using the Cerebellar vermis for an analysis with our PET data. Is the cerebellar vermis segmented during the FreeSurfer pipeline analysis? If it is, which file is it located in or how can I export a nifti file containing this segmentation? Thanks, Cyrus Sarosh [Description

Re: [Freesurfer] changes in tracula in the upcoming freesurfer release 5.2

Anastasia, We have a set of MR data and all have the recon-all processing done in FreeSurfer version 5.1. Will we be able to use the results from the recon-all FreeSurfer version 5.1 for the new TRACULA version 5.2 or will we have to run recon-all in version 5.2 to use TRACULA version 5.2? Tha

Re: [Freesurfer] Mssing Insula and mri_label2vol script

d). I am > still thinking that this is a compilation issue of the script, that is > just compiled for linux. > > Thanks for your help > > Try this one > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_labe > l2vol.linux32 > &g

Re: [Freesurfer] (no subject)

permissions to be executable? chmod a+x mri_label2vol doug On 12/04/2012 11:34 AM, Sarosh, Cyrus wrote: > > Doug, > > I am also curious about this mri_label2vol upgrade. Will this work on > the Windows virtual machine version of FreeSurfer? I downloaded and > placed it in

Re: [Freesurfer] (no subject)

Doug, I am also curious about this mri_label2vol upgrade. Will this work on the Windows virtual machine version of FreeSurfer? I downloaded and placed it in the FREESURFER/bin directory, but when trying to run it I receive an error that states: Exec format error. Binary file not executable. Tha

Re: [Freesurfer] Edits to aparc+aseg.mgz

[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, August 21, 2012 3:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Run it with -autorecon3 doug On 08/21/2012 10:44 AM, Sarosh, Cyrus wrote: > Doug, > > Thank

Re: [Freesurfer] Edits to aparc+aseg.mgz

brainmask.mgz, not brainmask.finalsurfs.mgz. Sorry about, I hope you did not waste too much time. doug On 08/20/2012 09:31 AM, Sarosh, Cyrus wrote: > Doug, > > I edited the dura from the brain.finalsurfs.mgz file using the command > tkmedit (subject ID) brain.finalsurfs.mgz -aux T1.mgz -sur

Re: [Freesurfer] Edits to aparc+aseg.mgz

it, you would edit the dura from the brain.finalsurfs.mgz and run recon-all with -autorecon-pial. This will fix aparc+aseg and re-generate the stats files. doug On 08/14/2012 01:40 PM, Sarosh, Cyrus wrote: > Doug, > > Well we want to use the stats information for gray matter v

Re: [Freesurfer] Edits to aparc+aseg.mgz

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Depending upon how bad it is and what you are going to do with it, it may be a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run recon-all -autorecon-pial ... doug On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote: > D

Re: [Freesurfer] Edits to aparc+aseg.mgz

08/13/2012 01:04 PM, Sarosh, Cyrus wrote: > > Hello FreeSurfer Users, > > I looked for a possible solution to my problem in the Mail Archive and found > this article referring to almost the exact same problem I am having: > http://www.mail-archive.com/freesurfer@nmr.mgh.harva

[Freesurfer] Edits to aparc+aseg.mgz

Hello FreeSurfer Users, I looked for a possible solution to my problem in the Mail Archive and found this article referring to almost the exact same problem I am having: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314.html. Basically, pieces of the subarachnoid space/pia ma

[Freesurfer] aparc+aseg labels

Hello, I was hoping somebody could help me out. I am trying to create a label file for the aparc+aseg file. All I'm wanting is the pixel value and the label. I know there is the FreeSurferColorLUT.txt file which contains this information, but looking at this file I can tell that all of these la

[Freesurfer] Running recon-all fails during autorecon-2 -careg step

I have run recon-all on multiple subjects and have had it fail at the same step every time with the same error. I am using VirtualBox with the provided Disk Image and Windows 7. 0560: dt=0.001750, rms=0.358 (0.039%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error.