[Freesurfer] poor grey/white distinction in superior part of scan

Hello, I am emailing to inquire about whether poor grey/white contrast in one part of a scan (i.e., the posterior and superior part of the scan; ~parietal cortex) can be addressed. The contrast in other parts of the scan looks good and freesurfer does a great job of distinguishing white from

[Freesurfer] recon-all finished with ERRORs

Hello, After successfully running a subject through freesurfer (recon-all -make all) several times as I fixed some pial and white matter edits, I now get the message that recon-all finished with errors. Inspection of the recon-all.log doesn't reveal any error messages to me in any particular

[Freesurfer] recon-all finished with ERRORs

See my original post at the end of this message and some more information included below. What would have been edited between the previous run without errors and the current run with errors is the brainmask, the wm.mgz file, and control points. On Tue, Oct 30, 2012 at 1:21 PM, Christine Smith

Re: [Freesurfer] recon-all finished with ERRORs

? We sometimes run 3 subjects at a time, but this does not exhaust our RAM or the number of processors. Christine On Wed, Oct 31, 2012 at 9:31 AM, Christine Smith cnsm...@ucsd.edu wrote: The command line was: recon-all -make -s CON1 I am not sure why the log said it was: recon-all -s /usr

[Freesurfer] entorhinal cortex excluded from wm.mgz and pial surface

Hello, I have a subject whose entorhinal cortex on one side of the brain is being excluded from the white matter surface and the pial surface. The cortex is included in the brain mask. I have tried a number of approaches to fix the problem but none have worked. First, I set some control points

[Freesurfer] talairach.xfm empty

Hello, I have a subject whose talairach.xfm file is present, but has no size (0 kb). I reran recon-all -talairach -s subject name. It does not fix the problem. The only error in that output was: error loading transform from /path to subject data/mri/transforms/talairach.xfm After rerunning the

[Freesurfer] poor image quality and re-running freesurfer

Hello, I have a couple of subjects with poor quality scans. The grey/white contrast is not so good. I wonder if the newest version of freesurfer might help with the pial and white surfaces. Do I need to make some minor edits to key images/files in order to force freesurfer to take a second shot