Thank everyone for very informative comments!
I am a newbie in freesurfer myself, I just got a dataset for the
analysis (data was preprocessed in freesurfer), and since I am moving
myself toward doing any analysis in python, and the tools I use now are
python libraries, I wanted to load the data in python.
What I got was
$> /bin/ls -R
.:
lh.exper_dossdintnoage.glmdir rh.exper.thickness.10.mgh
lh.exper.thickness.10.mgh rh.exper_dossdintnoage.glmdir
./lh.exper_dossdintnoage.glmdir:
ar1.mgh beta.mgh dossdintnoage eres.mgh fsgd.X.mat mri_glmfit.log
rstd.mgh rvar.mgh Xg.dat y.fsgd
./lh.exper_dossdintnoage.glmdir/dossdintnoage:
C.dat F.mgh gamma.mgh maxvox.dat sig.mgh
./rh.exper_dossdintnoage.glmdir:
ar1.mgh beta.mgh dossdintnoage eres.mgh fsgd.X.mat mri_glmfit.log
rstd.mgh rvar.mgh Xg.dat y.fsgd
./rh.exper_dossdintnoage.glmdir/dossdintnoage:
C.dat F.mgh gamma.mgh maxvox.dat sig.mgh
Also there is a directory on top
$> ls ../EXPERAVE/
4 label/ 0 mri/ 0 scripts/ 4 stats/ 4 surf/ 0 tmp/
for the avg subject
If I understand it right, .glmdir are just the result of glm analysis which I
am not interested in at the moment. I wanted to get thickness out, thus
{l,r}h.exper.thickness.10.mgh seemed the one I needed ;)
I'm not sure if they originally were in the proprietary format...
if I got it right mris_convert needs original mesh (lh.inflated) which
was used for the lh.exper.thickness.10.mgh. I have a few for avg subject, but I
am not sure which one (inflated or not) was used for generation of the
thickness or is the thickness mesh independent somehow?
On Thu, 24 Apr 2008, Nick Schmansky wrote:
> But I doubt that helps too much, since I'm guessing you want to avoid
> having to use the freesurfer binaries and want to just read the files
> directly.
well, I can leave with 1 time conversion ;) Having direct interface from python
is a neat thing to have though. by ldd on mris_convert and its size (3MB) I
guess freesurfer statically compiles in IO functionality in. It would be great
if there just was a dynamic library which does IO. Then it could be quite easy
to create python wrapper which would use it more or less directly...
> Nick
--
Yaroslav Halchenko
Research Assistant, Psychology Department, Rutgers-Newark
Student Ph.D. @ CS Dept. NJIT
Office: (973) 353-5440x263 | FWD: 82823 | Fax: (973) 353-1171
101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102
WWW: http://www.linkedin.com/in/yarik
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