[Freesurfer] tkmedit background color

Dear Freesurfer experts, I am trying to find out how to change the background color of tkmedit. Is there a possibility to change the background color from black to white, just for display purposes? (to avoid laborious photoshop work). Best Regards, Ruthger Righart

Re: [Freesurfer] mergecontrasts-sess group map

Hi Doug, So if I run a group analysis with each contrast separately, would I then be running mri_concat to do a conjunction of the group sig maps? Also, can I merge more than 2 contrasts at once when using mri_concat? Thanks! Alex Hi Alex, unfortunately, you cannot compute a conjunction with

Re: [Freesurfer] FW: TRACULA some fiber volumes being too small

Fantastic, thanks! On Fri, 30 Nov 2012, Fernando Ventrice wrote: Dear Anastasia, now it worked perfectly well changing the Z gradient with *(-1)! Here I send you a screenshot. Best, Fernando -Mensaje original- De: Fernando Ventrice Enviado el: 29 November 2012 11:39 Para: Anastasia

Re: [Freesurfer] p-value too small?

Hi Doug and Sebastian, thanks for your input. I think I can confirm that it is the problem that Sebastian described. FS 5.1 uses betainc, which returns 0, even in Matlab R2011b. The workaround that Sebastian suggested works, with a slight modification. In line 888 in fast_selxavg3.m currently

Re: [Freesurfer] p-value too small?

sorry, -log10(1) gives 0 of course. caspar 2012/11/30 Caspar M. Schwiedrzik cschwie...@rockefeller.edu: Hi Doug and Sebastian, thanks for your input. I think I can confirm that it is the problem that Sebastian described. FS 5.1 uses betainc, which returns 0, even in Matlab R2011b. The

Re: [Freesurfer] TRACULA tract path failure

Hi Arman - Yes, this looks like a tough one. This subject has mega-ventricles and a pretty thin, oddly shaped forceps minor. I can't actually test if this'll work b/c the bedpost directory is missing from the uploaded data, but can you please try changing the 2nd control point in this text

Re: [Freesurfer] mergecontrasts-sess group map

yesand yes doug On 11/30/2012 10:53 AM, Alexandra Tanner wrote: Hi Doug, So if I run a group analysis with each contrast separately, would I then be running mri_concat to do a conjunction of the group sig maps? Also, can I merge more than 2 contrasts at once when using mri_concat? Thanks!

Re: [Freesurfer] tkmedit background color

No, sorry, black is the only choice. doug On 11/30/2012 07:13 AM, Righart, Ruthger Dr. wrote: Dear Freesurfer experts, I am trying to find out how to change the background color of tkmedit. Is there a possibility to change the background color from black to white, just for display

Re: [Freesurfer] p-value too small?

Hi Caspar, On Nov 30, 2012, at 08:25 , Caspar M. Schwiedrzik wrote: Hi Doug and Sebastian, thanks for your input. I think I can confirm that it is the problem that Sebastian described. FS 5.1 uses betainc, which returns 0, even in Matlab R2011b. The workaround that Sebastian suggested

Re: [Freesurfer] p-value too small?

That should work. I just made a slightly different modification to the code, which will be in 5.2 pmat = FTest(dof1, dof2, Fmat); ind = find(rvarmat == 0); pmat(ind) = 1; % in case all time points are same value ind = find(pmat == 0);pmat(ind) = eps(0); % for REALLY sig

[Freesurfer] Public Supercomputing service to process FreeSurfer data

We are announcing today the release of the Public Beta of CerebralVol.comhttp://cerebralvol.com/, a public cloud based supercomputer service to process FreeSurfer data. CerebralVol.com users can process large amount of data using recon-all in a single day without the hassle of dealing with Unix

[Freesurfer] question on invoking partial volume calculations in freesurfer 4.3

Hello, My freesurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 I noticed that the aparc+aseg.mgz label map is resampled to 1mm x 1mm x 1mm voxels, eventhough the .mgz grayscale mri image file remains as per the original voxel size and is not 1x1x1. mri_convert .nii to .mgz

Re: [Freesurfer] question on invoking partial volume calculations in freesurfer 4.3

Hi John, it has been a long time since I looked at version 4.3, so I don't know if it can or not. One thing you can try is to use the version 5.x mri_segstats (the program which computes the aseg.stats table). You could run this outside of recon-all and generate a file with a different name.

Re: [Freesurfer] recon-all unable to make pial and white surfaces

Look like it is running out of memory. How much ram do you have on that machine? Bruce On Nov 30, 2012, at 9:29 PM, Negar Memarian negar.memar...@utoronto.ca wrote: Hello, I ran recon-all -all on my subject. The process ended after several minutes with this message at the end:

Re: [Freesurfer] question on invoking partial volume calculations in freesurfer 4.3

Thanks Doug. Do you know if the Freesurfer volumes in mm^3 that are posted on the ADNI website (particularly the longitudinal studies) include partial volume corrections? i.e., if they were run to include partial volume calculations? Thank you, John On 2012-11-30, at 3:11 PM, Douglas N Greve

Re: [Freesurfer] recon-all unable to make pial and white surfaces

Hi Bruce, I have 8 GB ram and have assigned 6GB of it to FreeSurfer. Shall I increase it to 8? Would that be enough or still too low? Thank you, Negar On Fri, Nov 30, 2012 at 7:31 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Look like it is running out of memory. How much ram do you have