Now I remember why I couldn't do the mris_convert thing. Perhaps someone has a solution.
mris_convert, if I run it on an image, requires a surface file in order to turn it into an ascii file. For instance, I can't just run: mris_convert sph-f-lh.img sph-f-lh.asc or mris_convert -c sph-f-lh.img sph-f-lh.asc I would have to run something like: mris_convert -c sph-f-lh.img $SUBJECTS_DIR/subj/lh.sphere ./lh.sph-f-lh.asc or something like that.
The problem is that if sph-f-lh.img is registered using --trgsubject ico, then I have no surf file with which to convert my image into ascii. So what do I do in that case?
Thanks, -Alessandro
On 4/4/07, Alessandro Gagliardi alessandro@gagliardi.name wrote:
I ended up trying a bit of a hack, and it seems to have worked, but I don't know if I can trust it. I used the AnalyzeFMRI package in R to output my data in an Analyze file. I had to change the voxel size and origin in the header manually. And then I copied a .mat file from another 3D Analyze file produced by FreeSurfer with the same dimensions as my output and named it the same as my new Analyze file. I don't really know how the .mat file works, so as I said, I don't know if I can trust it. The .mat file is from a the same data that I'm analyze in R, so it should have the same orientation. Perhaps one of the FreeSurfer gurus can tell me if this is a really stupid thing to do or not.