Re: [Freesurfer] center of pial surface in world coordinates

Hi Doug,Thanks for your reply. Indeed, I can open the surface in both programs, but there seems to be a shift in a coordinate system. I want to plot fiber tracts in Neurolens as well, so I need to know where I can find the exact (0,0,0) coordinate in the pial surface. Using tksurfer the (0,0,0) coo

Re: [Freesurfer] converting .img to .mgz

That doesn't seem to work...the error it gives is > > "Unsupported datatype 132" --- Doug Greve <[EMAIL PROTECTED]> wrote: > > You can't use .img files directly in the recon. The > cmd line you have > will work, or you can > > mkdir -p subject_name/orig > mri_convert raw.img subject_name/orig

Re: [Freesurfer] FSL output overlay

What do you mean "to get proper output from reg-feat2anat"? This program produces a freesurfer registration file, which you then check with reg-feat2anat --manual ... doug Vishwadeep Ahluwalia wrote: Hi, To elaborate my problem a little more ... Running FSL command avwhd gave me : filena

Re: [Freesurfer] converting .img to .mgz

You can't use .img files directly in the recon. The cmd line you have will work, or you can mkdir -p subject_name/orig mri_convert raw.img subject_name/orig/001.mgz Note: make sure that you look at 001.mgz in tkmedit to make sure that it is oriented correct, esp if the .img does not have a .

Re: [Freesurfer] converting .img to .mgz

that should work. Why do you want another way? Bruce On Thu, 8 Jun 2006, Chacko Cherian wrote: Hi everybody, I ve got a small question on converting .img scans(Analyze) TO .mgz... suppose i have a raw.img(and raw.hdr) file and I want to use recon-all for converting this to .mgz do I just ne

[Freesurfer] converting .img to .mgz

Hi everybody, I ve got a small question on converting .img scans(Analyze) TO .mgz... suppose i have a raw.img(and raw.hdr) file and I want to use recon-all for converting this to .mgz do I just need to do recon-all -i raw.img -s Or is there any other way I can directly use .img files instead

[Freesurfer] FSL output overlay

Hi, To elaborate my problem a little more ... Running FSL command avwhd gave me : filename spiral.nii.gz sizeof_hdr 348 data_type INT16 dim0 4 dim1 64 dim2 64 dim3 25 dim4 250 dim5 1 dim6 1 dim7 1 vox

Re: [Freesurfer] center of pial surface in world coordinates

Hi Martijn, we still support COR. I'm at a disadvantage here in that I've not used Neurolens before. I'm not even sure what the problem is. You can show the surfaces in neurolens and in tksurfer, so what's the problem? doug martijn van den heuvel wrote: Dear Bruce, Thanks for your quick r

Re: [Freesurfer] FS on Fedora Core 5, GLXBadLargeRequest

Glenn, You are correct in finding that just the tksurfer app is the one binary from the standard centos4_x86_64 stable freesurfer build that does not work on fc5. By coincidence, I have been working with a 32bit FC5 platform, and found that this is true.  That is, the standard centos4 stable

Re: [Freesurfer] tksurfer hemodynamic waveforms for group analysis

If you're still having trouble with the time course loading, can you send me the command line you're using and the data you are trying to load? On Wed, Jun 07, 2006 at 07:35:49PM -0400, Doug Greve wrote: > > It is definitely possible to display time courses in tksurfer, but I > usually load the

[Freesurfer] FS on Fedora Core 5, GLXBadLargeRequest

Hi, Around the 25th of April there was a brief discussion regarding running FreeSurfer on a FC5 machine. Some users were having a problem with tksurfer not displaying and an error with the X server (GLXBadLargeRequest). I just installed the centos _x64 3.0.3 verson of FreeSurfer on a FC5 mac