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