Re: [Freesurfer] Freesurfer flips brains?

2012-01-20 Thread Frank
Hi everyone, Just a quick word of warning (plus two follow-up questions): there are more instances where your brain can get flipped. For example, I just regenerated my surface, using the correct orientation, certain about that. If I then do bbregister afterwards using the structural I convert

[Freesurfer] Re-generating spherical surfaces...

2012-01-20 Thread Rudolph Pienaar
Hi all -- If I make changes to a subject's ?h.smoothwm, how do I re-generate the ?h.sphere surfaces? I'd like to reduce the number of mesh vertices using 'mris_decimate' on a given hemisphere, and then (re)generate a corresponding spherical surface. Thanks -- Rudolph Pienaar, M.Eng, D.Eng /

Re: [Freesurfer] Re-generating spherical surfaces...

2012-01-20 Thread Douglas N Greve
Hi Rudolph, try recon-all -sphere -s subject or run mris_sphere doug Rudolph Pienaar wrote: Hi all -- If I make changes to a subject's ?h.smoothwm, how do I re-generate the ?h.sphere surfaces? I'd like to reduce the number of mesh vertices using 'mris_decimate' on a given hemisphere,

[Freesurfer] QATools

2012-01-20 Thread Irwin, William
Hi - The link to download the QATools script (http://surfer.nmr.mgh.harvard.edu/fswiki/QATools) for non-MGH users is broken, and I couldn't find it by looking through the ftp download directories. Regards, Wil ___ Freesurfer mailing list

[Freesurfer] qdec analysis

2012-01-20 Thread Cat Chong
Hello Experts: In qdec, I would like to analyze if the thickness- entorhinal volume correlation differs between APOE positive and negative subjects accounting for age. I have chosen age as a nuisance variable and entorhinal volume as a covartiate. ( hope this is correct) Results show me

Re: [Freesurfer] memory allocation error with mris_register

2012-01-20 Thread Arno Klein
dear doug, i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0. i am only having this trouble for one of the subjects. after the mri_convert workaround i am still getting the same memory allocation error. cheers, @rno On Fri, Jan 20, 2012 at 4:23 PM, Douglas N Greve

Re: [Freesurfer] Freesurfer flips brains?

2012-01-20 Thread Douglas N Greve
Hi Frank, I think this problem is only spm related when using bbregister with the --init-spm option. This will in no way affect the anatomical analysis. According to my notes, this happens with spm8 when it uses analyze format. analyze is the default format used intermediate files by

Re: [Freesurfer] memory allocation error with mris_register

2012-01-20 Thread Douglas N Greve
Try doing it in matlab, so a = MRIread('orig.mgz'); MRIwrite(a,'orig.mgz'); doug Arno Klein wrote: dear doug, i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0. i am only having this trouble for one of the subjects. after the mri_convert workaround i am still getting

Re: [Freesurfer] memory allocation error with mris_register

2012-01-20 Thread Arno Klein
dear doug, sadly, no dice. cheers, @rno On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Try doing it in matlab, so a = MRIread('orig.mgz'); MRIwrite(a,'orig.mgz'); doug Arno Klein wrote: dear doug, i am using FS v5.1 now but ran the 20 oasis

Re: [Freesurfer] memory allocation error with mris_register

2012-01-20 Thread Louis Nicholas Vinke
Hi Arno, Please give these matlab commands a shot. [v,M, mr] = load_mgh('orig.mgz'); save_mgh(v, 'orig.mgz', M, mr); -Louis On Fri, 20 Jan 2012, Arno Klein wrote: dear doug, sadly, no dice. cheers, @rno On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Greve

Re: [Freesurfer] memory allocation error with mris_register

2012-01-20 Thread Bruce Fischl
can you load the lh.sphere in tksurfer? I'm not sure it is the mgz file that is the problem. Maybe your partition filled up and the sphere file isn't complete? On Fri, 20 Jan 2012, Arno Klein wrote: dear doug, sadly, no dice. cheers, @rno On Fri, Jan 20, 2012 at 4:45 PM, Douglas N

Re: [Freesurfer] memory allocation error with mris_register

2012-01-20 Thread Arno Klein
dear bruce, you're right -- i am able to view the pial surface, but when i try to view the spherical surface with tksurfer i get the same memory error. is there any way to fix the sphere without affecting anything else? neuromorphometrics has painstakingly manually edited the freesurfer labels

Re: [Freesurfer] memory allocation error with mris_register

2012-01-20 Thread Bruce Fischl
you can just rerun the mris_sphere command that is in the recon-all.log (or recon-all.cmd) cheers Bruce On Fri, 20 Jan 2012, Arno Klein wrote: dear bruce, you're right -- i am able to view the pial surface, but when i try to view the spherical surface with tksurfer i get the same memory

Re: [Freesurfer] QATools

2012-01-20 Thread Louis Nicholas Vinke
Hi Wil, Sorry about that, the link is now fixed with the most recent version of the QAtool scripts. -Louis On Fri, 20 Jan 2012, Irwin, William wrote: Hi - The link to download the QATools script (http://surfer.nmr.mgh.harvard.edu/fswiki/QATools) for non-MGH users is broken, and I

[Freesurfer] Per-run registration in monkey fmri

2012-01-20 Thread SHAHIN NASR
Hi In monkey fmri, we usually have to do the functional-anatomical registration manually since bbregister doesn't work very well. It was easy in version 4.5 since we usually used just one run for registration. In version 5.1 we can use per-run option to improve registration but I am