[Freesurfer] BEM surfaces

Dear experts, Currently I am playing around with the mri_watershed algorithm. After processing the T1.mgz from "bert" I got 256 COR files plus the COR-.info with the direction cosine information. Output in bert/bem/: COR-.info, COR-001 . COR-256 How can extract the information of t

[Freesurfer] normal brain volume ?...

Hi: I am quantifying the brain volume of some MS patients (BrainSegVol-ventricles-cerebelum-brain_stem)... There exist any paper that shows normal brain volume ?... There exisst any other way to compute the brain volume ?... Sincerely, Gonzalo Rojas Costa

Re: [Freesurfer] QDEC 5.0 with data from 4.x recon-all data

You can say 4.x. The statistical part did not change that much in version 5. doug Manabu Kubota wrote: > Hi, > > I'm interested in this issue. > If I use a former FreeSurfer version (ver. 4.x) for all the > preprocessing of each data and apply the new QDEC in FreeSurfer ver. > 5.0.0 JUST to ma

Re: [Freesurfer] Freesurfer Digest, Vol 79, Issue 32

Siti, can you give us the full command-line (without the variables) and the full terminal output? doug Siti Hajar wrote: > When I ran this command, " mri_segstats --seg > "$fsaveragesurfpath"/"$hemi".fsaverage."$hemi"_"$roi"_"$subj".mgh --in > "$hemi".thickness.fsaverage.mgh --sum > segstats-

Re: [Freesurfer] problem with tksurfer display

Have you tried updating your video driver? What kind of video card to you have? On Sat, 2 Oct 2010, [gbk] ²ýÃ÷ wrote: Dear Freesurfers£º When I display and edit surfaces with tksurfer, the image can be loaded correctly, but whenever i rotate it, load curvatures, or load patches, it always

Re: [Freesurfer] Retinotopic mapping of only polar data

Old topic, but it is directly related, so I'll just continue it here. In the end I have the spots on the right place, but now it's not clear to me how to interpret the map. I have created three overlays (sign, log10 * sin, log10 * cos, like mentioned in selfreq.pdf) and loaded them all three in tk

Re: [Freesurfer] spmregister error

Chindhuri, Is the path to spm2 added in your startup.m file and are you using matlab 7.1 (required by spm2)? doug Chindhuri Selvadurai wrote: > Hello, > > I am getting the same error that was discussed in the attached thread, > however, the addition of the path line did not work for me. > > I a

Re: [Freesurfer] spmregister error

Hello, I am getting the same error that was discussed in the attached thread, however, the addition of the path line did not work for me. I am also not sure if we should be using spm5 since all in the past we have been using spm2. It presents this error when running under my name, but not for oth

Re: [Freesurfer] Making a surface from the skull?

Thanks for these suggestions - looks promising so far! mjp On Oct 1, 2010, at 4:32 PM, Nick Schmansky wrote: > also, once you get a surface file, then mris_convert will convert > to .stl format, which we've used in 3d printer applications. > > if you can get a skull from mri_watershed, then mri

[Freesurfer] Are cortical thickness and surface area independent of each other?

Dear FS experts I would like to know whether cortical thickness and cortical surface area as computed by FS are independent of each other. My guess is that they are not independent, isn't it? Regards Jürgen Jürgen Häng

Re: [Freesurfer] Are cortical thickness and surface area independent of each other?

do you mean independent in the statistical sense? Certainlty the way in which they are computed is independent, and in principle they should not depend on each other cheers, Bruce On Mon, 4 Oct 2010, Jürgen Hänggi wrote: Dear FS experts I would like to know whether cortical thickness and