[Freesurfer] no CSF

when running mris_make_surfaces it's possible to manually set CSF,GM,WM and related thresholds. now, what of the case where one simply doesn't have any CSF? i.e. an ex-vivo scan. I find it really hard to get a good pial surface despite much experimentation. It wants to contract the GM and make t

[Freesurfer] file conversion

also - I'm assisting someone with a dti analysis. the data I have is a martinos centre .hdr .bshort file, acquired at martinos I think, in 2005. I'm having trouble figuring out how to covert this (mainly for use with FSL) I'd like a 4d nifti ultimately (or analyse). I was thinking of writing code

[Freesurfer] mris_fix_topology stops with two T1-s

Hi FS experts, I've run recon-all -i file -s subject -qcache -measure thickness -all to: - 18 subjects, session 1 T1 - same 18 subjects, session 2 T1 and everything went well. Then I copied the /mri/orig/001.mgz-s to /mri/orig/001.mgz and 002.mgz, and run the same command again: recon-all -s

Re: [Freesurfer] no CSF

Thanks Ritobrato yes, I'm aware of this. the trouble is I can't get it right to my satisfaction. I tried a lot! my problem is finding the right parameters that you show below. My experience (since you have not tired yet) is that you will have to use these parameters, absolutely. you have to mes

Re: [Freesurfer] mris_fix_topology stops with two T1-s

Hi Gari is it still running? The time it takes is square in the convex hull of the largest defect, so that can take a long time. A 45K defect is too big and typically means something is dramatically wrong, like the cerebellum or skull is attached. cheers Bruce On Sun, 5 Aug 2012, Garikoitz