[Freesurfer] Regression analysis on files produced with the -osgm flag

Dear FS experts We have done a one-sample-group-mean (osgm) analysis and now we would like correlate a behavioural measure with the difference maps produced by the -osgm analysis. Is this possible? Or do we have to compute the difference of each subject again, the running mri_surf2surf to regist

[Freesurfer] Watershed Errors - Multiple attempts tried

Hi all, I'm assissting with an aging study and a good handful of their scans are coming up with watershed errors. My assumption was errors with the skull strip leading to empty brain volumes. I have read through all the lists and tried the following: - Manually corgistering to MNI to improve T

Re: [Freesurfer] Watershed Errors - Multiple attempts tried

Hi Christian, do you mean a T1 map? Have you tried T1 weighted (is that T1w?)? What sequence is it? If you are really seeing high error rates with T1 weighted images you are welcome to drop some on our site and we'll take a look. cheers, Bruce On Tue, 6 Jul 2010, Christian Lambert wrote: > Hi

[Freesurfer] Post-doctoral Position in Vascular Dementia Research at the German Center for Neurodegenerative Diseases (DZNE) in Munich

Post-doctoral Position in Vascular Dementia Research at the German Center for Neurodegenerative Diseases (DZNE) in Munich The German Centre for Neurodegenerative Diseases (www.dzne.de) has been newly founded by the Helmholtz Foundation. The DZNE Munich is now offering a post

[Freesurfer] Spatial info of vertices

Hi all, I'm hoping to extract the connections and distances (edge and weight) of the vertices for each of my individual subjects' surfaces. How can I go about doing this? Thanks! Nathan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu htt

Re: [Freesurfer] Spatial info of vertices

Hi Nathan, reading them into matlab would be the easiest way I think. Thomas Yeo (ccd) has matlab code for computing L1 distances on the surfaces. cheers Bruce On Tue, 6 Jul 2010, Dankner, Nathan (NIH/NIMH) [F] wrote: > Hi all, > > I'm hoping to extract the connections and distances (edge an

Re: [Freesurfer] Qdec - problem with the Generate Stats Data Import button.

Hi Gaelle This seems to be an error due to Python's "warning" module being deprecated in Python 2.6. I'll update the sources so as to accommodate this change. Meanwhile, the quickest fix is to open up nano $FREESURFER_HOME/bin/asegstats2table and comment out the following lines ( put a "#"

[Freesurfer] Any update on releasing the source for FreeSurfer?

Hey Everyone, I searched through the archives and it seems to be that there is an intent to release FreeSurfer as open source eventually. However, the most recent post about that that I could find was from a year or two ago. Is there any update on this or plan for when this will happen?

Re: [Freesurfer] Any update on releasing the source for FreeSurfer?

Hi Alex, you're welcome to a source distribution now. Nick can get you one. cheers Bruce On Tue, 6 Jul 2010, Alex Waite wrote: > Hey Everyone, > I searched through the archives and it seems to be that there is an > intent to release FreeSurfer as open source eventually. However, the > mos

Re: [Freesurfer] Any update on releasing the source for FreeSurfer?

Excellent! This is all very good news. Is it Nick Schmansky I should be contacting? If so, I'll shoot him an email. Thanks for the quick response. ---Alex On 07/06/2010 01:06 PM, Bruce Fischl wrote: > Hi Alex, > > you're welcome to a source distribution now. Nick can get you one. > >

Re: [Freesurfer] Any update on releasing the source for FreeSurfer?

Hi, On Tue, Jul 06, 2010 at 02:06:36PM -0400, Bruce Fischl wrote: > Hi Alex, > > you're welcome to a source distribution now. Nick can get you one. That sounds great -- what license will it be under? Thanks in advance, Michael -- GPG key: 1024D/3144BE0F Michael Hanke http://mih.voxindeser

Re: [Freesurfer] Any update on releasing the source for FreeSurfer?

the source is still not truly open source yet, its available under the existing terms (non-commercial, non-clinical, academic-only). our intention is to create a BSD-style open source release. n. On Tue, 2010-07-06 at 14:22 -0400, Michael Hanke wrote: > Hi, > > On Tue, Jul 06, 2010 at 02:06:36P

Re: [Freesurfer] Any update on releasing the source for FreeSurfer?

Nick, the 5.0 will be non-clinical? -- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- For mobile: http://www.netfilter.com.br/mobile On Tue, Jul 6, 2010 at 16:05, Nick Schmansky wrote: > the sourc

Re: [Freesurfer] Any update on releasing the source for FreeSurfer?

Hi PPJ, yes, that's currently out of our control (due to CorTechs licensing constraints). BSD would be nice some day, but not something we can do at the moment. cheers Bruce On Tue, 6 Jul 2010, Pedro Paulo de Magalhães Oliveira Junior wrote: Nick, the 5.0 will be non-clinical?

[Freesurfer] surface-based cytoarchitectonic map

Hi Freesurfer users, In the paper, "Cortical folding patterns and predicting cytoarchitecture" by Fischl et al (Cerebral Cortex, 2008), it's mentioned that "surface-based probabilistic maps of the cytoarchitectonics can be downloaded from http://surfer.nmr.mgh.harvard.edu/fswiki";. I can't seem t

Re: [Freesurfer] Any update on releasing the source for FreeSurfer?

Hi Alex I'm running fs on debian boxes here and they run the freesurfer-Linux-centos4-stable-pub-vX.X.X version, without any need to recompile sources cheers > Hey Everyone, > I searched through the archives and it seems to be that there is an > intent to release FreeSurfer as open sourc

Re: [Freesurfer] surface-based cytoarchitectonic map

Hi Danny, you probably already have them, but they will be automatically generated in the upcoming V5. You can see if your recon-all supports -balabels. cheers, Bruce On Tue, 6 Jul 2010, Danny Kim wrote: > Hi Freesurfer users, > > In the paper, "Cortical folding patterns and predicting cytoarc