Re: [Freesurfer] Extraction of WM + GM Volumes

2009-09-01 Thread Ed Gronenschild
Doug, I want all GM. Ed On 26 Aug, 2009, at 18:53 , freesurfer-requ...@nmr.mgh.harvard.edu wrote: For WM, you can use aparc+aseg.mgz and use indices 2 and 41. Do you want a particular GM or all GM? Ed Gronenschild wrote: Doug, The file "segmentation.mgz" doesn't exist. I think that

[Freesurfer] Problem with topology fixing

2009-09-01 Thread Ed Gronenschild
Hi, I got the following error during processing my subject nr 104 with recon-all: ERROR: - FindPacePath: could not find path. The error log tells that it occurred during execution of the command mris_topo_fixer -mgz -warnings 104 rh What to do? Ed __

Re: [Freesurfer] Problem with topology fixing

2009-09-01 Thread Bruce Fischl
did you try using the old (default) topology fixer? Usually mris_fix_topology is called in recon-all unless you specify otherwise. cheers, Bruce On Tue, 1 Sep 2009, Ed Gronenschild wrote: > Hi, > > I got the following error during processing my subject nr 104 with > recon-all: > > ERROR: - Find

Re: [Freesurfer] Input/Output to specific atlas space/dimensions?

2009-09-01 Thread Alexander Li Cohen
Has anyone had a chance to take a further look at the output differences in using the -mprage option yet? (I'm still new at freesurfer and probably wouldn't know what to look for...) -Alex ~)--- -- Alexander Li Co

Re: [Freesurfer] Problem with topology fixing

2009-09-01 Thread Ed Gronenschild
Hi Bruce, The log file tells that mris_fix_topology did fail (euler number != 2) and that's why the topo_fixer was used. Ed On 1 Sep 2009, at 15:12, Bruce Fischl wrote: > did you try using the old (default) topology fixer? Usually > mris_fix_topology is called in recon-all unless you specify ot

Re: [Freesurfer] Problem with topology fixing

2009-09-01 Thread Bruce Fischl
I see. Have you looked at the orig.nofix surface? If there is a huge defect (e.g. cerebellum or skull connected to cortex) then things will fail. Make sure nothing is dramatically wrong with it or the aseg.mgz first. Bruce On Tue, 1 Sep 2009, Ed Gronenschild wrote: > Hi Bruce, > > The log f

Re: [Freesurfer] Problem with topology fixing

2009-09-01 Thread Ed Gronenschild
Bruce, You're right: the skullstripping didn't go well so that part of the skull is still present. I'll try to fix that. Thanks, Ed On 1 Sep 2009, at 16:03, Bruce Fischl wrote: > I see. Have you looked at the orig.nofix surface? If there is a huge > defect (e.g. cerebellum or skull connected to

[Freesurfer] FreeSurfer_volume_Talairach

2009-09-01 Thread Judit Haasz
I assume my question has been skipped. sorry for bothering you again! Hi, I am trying to extract Talairach coordinates belonging to white matter volumes (wmparc subregions). Although tkmedit gives the coordinates for volumes, so far I have not found a feasible way by which I could print out th

[Freesurfer] tksurfer failures

2009-09-01 Thread Matt Sutterer
Hi all, I've tried running tksurfer to look at inflated hemispheres, and I can't seem to get my computer (or other machines for that matter) to show the entire inflated surface. All i get is a small bit of occipital cortex (that moves around and refreshes just fine), but I can't seem to get anyth

Re: [Freesurfer] tksurfer failures

2009-09-01 Thread Donna Dierker
I haven't experienced this with Freesurfer, but I have had this problem with Caret using Linux workstations with pre-installed NVIDIA drivers that were apparently not working correctly. Downloading and re-installing the NVIDIA driver corrected the problem on my Linux box. On 09/01/2009 01:32 P