Re: [Freesurfer] freeview problem

Thank you Zeke. I am trying to run freeview remotely and display locally on a machine (using Xming). The computer from which I am connecting can successfully run freeview from a different ubuntu 13 machine (one which does not have a cuda graphics card / cuda drivers). When I run glxgears (required

Re: [Freesurfer] Talairach error - Talairach file seems to not be written correctly.

Hi Bruce. Not that I can see. And it did create the talairach.xfm, but that file is missing the header for some reason. I'll send the log just as soon as I'm in tomorrow and I'll include the xfm file as well. Thanks so much for the help. -John Sent from my Windows Phone _

Re: [Freesurfer] Talairach error - Talairach file seems to not be written correctly.

Hi John can you send the entire recon-all.log? Any indication why the talairach.xfm was not created? cheers Bruce On Sun, 18 Aug 2013, West, John D. wrote: > Hello. > > We are trying to run freesurfer on a Super Computing system here at IU. > Unfortunately, we keep running into the following

Re: [Freesurfer] Longitudinal Two stage model limitations

Thanks very much for your help Martin ! of course we cite both NeuroImage papers, 2012 and 2010 in the description of methods. Have a great week ! Alex. Le 18/8 19:37 Martin Reuter a écrit : Yes sounds good. Maybe say "depending on the number and spacing of time points" . As distance in ti

Re: [Freesurfer] Longitudinal Two stage model limitations

Yes sounds good. Maybe say "depending on the number and spacing of time points" . As distance in time is also important. And maybe you want to cite our longitudinal paper 2012 neuroimage within subject template ... Good luck with your paper.  Best Martin Sent via the Samsung Galaxy S™ III, a

[Freesurfer] Talairach error - Talairach file seems to not be written correctly.

Hello. We are trying to run freesurfer on a Super Computing system here at IU. Unfortunately, we keep running into the following error: # #@# Talairach Failure Detection Sun Aug 18 14:17:32 EDT 2013 /N/dc/projects/shenlab/subjects/10025_5/mri talai

[Freesurfer] Trouble with mris_label2annot

Hello, I have a set of custom labels and I want to plot them all at once on one brain, so I'm trying to use mris_label2annot for that. However, I'm getting several problems. Here is an example of what I get: http://i.imgur.com/Sw1Z9UT.png The labels I'm using were originally defined on a decimat

Re: [Freesurfer] Robust brain extraction using Freesurfer

Hi Sourena the pial surface generation is pretty close to the end of recon-all, so you are probably better off just running the whole thing cheers Bruce On Sun, 18 Aug 2013, Sourena Soheili-Nezhad wrote: > Hello Freesurfer community > > I am trying to perform a voxelwise longitudinal analysis

Re: [Freesurfer] mris_thickness threshold

Hi Giusy they look pretty similar, no? The thickness is the average of two numbers (white->pial and pial->white) distances, so I think if either was originally greater than the max it will change when you change the max cheers Bruce On Sun, 18 Aug 2013, Giusy Chinnici wrote: Hi all, I'd l

[Freesurfer] Robust brain extraction using Freesurfer

Hello Freesurfer community I am trying to perform a voxelwise longitudinal analysis (outside FS). I have been searching for brain extraction algorithms and it seems that Freesurfer provides the most accurate solution. If the primary objective is highest accuracy, should I use recon-all products pr