Re: [Freesurfer] wm- volume limitations

Great - just what I was looking for - thanks. Regards, Don [Signature0001] Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On

[Freesurfer] Make liberal ROI masks

Dear all, I've created non-overlapping ROI masks using mri_label2vol --seg aparc.a2009s+aseg.mgz --regheader orig.mgz --o rois.nii --temp sub.nii --subject 01 Now these ROI masks are actually quite conservative concerning grey matter vs. other structures, i.e. they are only on the grey matter. I

Re: [Freesurfer] convert FS volume in scanner space

My command line was cd $SUBJECTS_DIR//mri mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz --no-save-reg according to fswiki/FsAnat-to-NativeAnat. As I mentioned, I am happy with the results but the coordinates are still RAS (from my understanding) and di

[Freesurfer] mris_fill on HCP data

Hi all, I have been trying to use the mris_fill function on some Human connectome project data. I firstly convert the .gii file containing the pial surface using mris_convert. When visualising the converted mesh into FreeView everything looks normal. After the first step (“mris_fill -c -r 1”),

Re: [Freesurfer] convert FS volume in scanner space

what do you mean the coords are still in RAS? On 7/8/15 8:25 AM, von Polier, Georg wrote: > My command line was > > cd $SUBJECTS_DIR//mri > mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o > brain-in-rawavg.mgz --no-save-reg > > according to fswiki/FsAnat-to-NativeAnat. > > As I me

Re: [Freesurfer] convert FS volume in scanner space

Sorry for the confusion: According to the presentation fswiki/CoordinateSystems (below) I meant, the data are in native space/ RAS, with coordinate center not at magnet center, which is what I need. Scanner Space - coordinate center at magnet isocenter, bore axis is Z, X to the left, Y to the

[Freesurfer] Cannot launch tkmedit in Ubuntu

Hello, When trying to use tkmedit, I got the following error message: No protocol specified No protocol specified GLUT: Fatal error in tkmedit.bin: could not open display: :0.0 In addition, when I tried to switch to freeview instead, I also got an error message: No protocol specified No protocol

Re: [Freesurfer] mris_fill on HCP data

Hi Matteo what happens if you use our surface format? Does it work properly? Bruce On Wed, 8 Jul 2015, Matteo Bastiani wrote: Hi all, I have been trying to use the mris_fill function on some Human connectome project data. I firstly convert the .gii file containing the pial surface using mr

Re: [Freesurfer] Cannot launch tkmedit in Ubuntu

Hi Yifan are you on the console of that machine or are you remotely logging in from somewhere else? Can you run standard x apps (like xclock)? cheers Bruce On Wed, 8 Jul 2015, Hu, Yifan wrote: Hello,   When trying to use tkmedit, I got the following error message: No protocol specifie

Re: [Freesurfer] mris_fill on HCP data

Hi Bruce, yes. With both surfaces (the original hcp '*.pial.surf.gii’ and the one I obtain using mris_converted '*.pial') I have the same results. To convert the original hcp gift surface into freesurfer format, I use: mris_convert subjId.surf,gii subjId.pial Is that the correct way? Cheers, M

Re: [Freesurfer] mris_fill on HCP data

do you have access to the surfaces before they were converted to gii? On Wed, 8 Jul 2015, Matteo Bastiani wrote: Hi Bruce, yes. With both surfaces (the original hcp '*.pial.surf.gii’ and the one I obtain using mris_converted '*.pial') I have the same results. To convert the original hcp gif

Re: [Freesurfer] mris_fill on HCP data

Nope. > On 8 Jul 2015, at 17:06, Bruce Fischl wrote: > > do you have access to the surfaces before they were converted to gii? > > On Wed, 8 Jul 2015, Matteo Bastiani wrote: > >> Hi Bruce, >> >> yes. With both surfaces (the original hcp '*.pial.surf.gii’ and the one I >> obtain using mris_

Re: [Freesurfer] mris_fill on HCP data

If you can you upload your subject on our website and email us the exact command lines you used, we will take a look. Bruce On Wed, 8 Jul 2015, Matteo Bastiani wrote: Nope. On 8 Jul 2015, at 17:06, Bruce Fischl wrote: do you have access to the surfaces before they were converted to gi

Re: [Freesurfer] Help with V6

Thanks Noah. It doea say on the website that you need the 2012b runtime, but its definitely buried among too much other, less critical stuff Cheers E Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disc

Re: [Freesurfer] 3 Group comparison

There is not a --meas option for mri_glmfit, you need to give it a --y option explicity, though it may be trying to read a yfile if you have one in the FSGD. How did you make g3v0.fsgd? Can you send it? The second command looks like you are doing the right thing, you just need to tell mri_glmfi