Forgive me if I'm simply missing the obvious, but as far as I can tell, mri_surf2surf is not capable of writing output in *any* of the surface formats listed in the Freesurfer surface formats document on the wiki, except .w paint format. Also, mris_convert doesn't accept .w as input; so there's no way at all to get output from mri_surf2surf into ascii format?
I'm also confused about why mri_surf2surf only writes out in volume formats like analyze and mgh (other than .w). If there are surface versions of these filetypes, where can I find documentation about those other surface formats, since they're not in the existing surface formats document?
Actually, this is all extra confusing because the output of --help for mri_surf2surf conflicts with the documentation on the wiki. The wiki says output can be curv format; the --help says not. It doesn't seem to be possible. Also some of the options have different names in the two locations.
Just out of curiosity, why does it work like that? I'd think it would make more sense simply to have it write out in the standard surface formats (surface or curv or ascii)...
All I'm trying to do is to subtract one set of curv-format data from another. (I have cortical thickness measures for the same subjects at two different times, and I want to be able to see the changes for individual subjects.) I have successfully registered the time 1 data onto the time 2 surface, and I can visualize it overlaid no problem. But I am struggling to find a way to subtract the aligned data... which seems like it should be easy... which makes me think I'm missing something obvious, but I've been searching through documentation for hours. I can see how to do it with Matlab, using mri_surf2surf to generate .w format output and reading it into Matlab, but I was hoping there would be a more straightforward way...
Also, as an aside, the comments for read_wfile.m are actually the comments for write_wfile.m. -- -dave---------------------------------------------------------------- After all, it is not *that* inexpressible. -H.H. The Dalai Lama
Hi David,
try mris_thickness_diff, or you can do it in matlab if you've resampled onto the same subject. The plethora of formats is for historical reasons, and we're slowly working our way through and rationalizing the binaries.
cheers, Bruce
On Sun, 6 May 2007, David Perlman wrote:
Forgive me if I'm simply missing the obvious, but as far as I can tell, mri_surf2surf is not capable of writing output in *any* of the surface formats listed in the Freesurfer surface formats document on the wiki, except .w paint format. Also, mris_convert doesn't accept .w as input; so there's no way at all to get output from mri_surf2surf into ascii format?
I'm also confused about why mri_surf2surf only writes out in volume formats like analyze and mgh (other than .w). If there are surface versions of these filetypes, where can I find documentation about those other surface formats, since they're not in the existing surface formats document?
Actually, this is all extra confusing because the output of --help for mri_surf2surf conflicts with the documentation on the wiki. The wiki says output can be curv format; the --help says not. It doesn't seem to be possible. Also some of the options have different names in the two locations.
Just out of curiosity, why does it work like that? I'd think it would make more sense simply to have it write out in the standard surface formats (surface or curv or ascii)...
All I'm trying to do is to subtract one set of curv-format data from another. (I have cortical thickness measures for the same subjects at two different times, and I want to be able to see the changes for individual subjects.) I have successfully registered the time 1 data onto the time 2 surface, and I can visualize it overlaid no problem. But I am struggling to find a way to subtract the aligned data... which seems like it should be easy... which makes me think I'm missing something obvious, but I've been searching through documentation for hours. I can see how to do it with Matlab, using mri_surf2surf to generate .w format output and reading it into Matlab, but I was hoping there would be a more straightforward way...
Also, as an aside, the comments for read_wfile.m are actually the comments for write_wfile.m. -- -dave---------------------------------------------------------------- After all, it is not *that* inexpressible. -H.H. The Dalai Lama
David,
To get the thickness data in ascii format, from the subjects 'surf' directory, type:
mris_convert -c lh.thickness \ lh.white lh.thickness.asc
where in the output file lh.thickness.asc each row contains:
vertex_num x y z thickness
When comparing two surfaces, the data from one surface will need to be sampled onto the other so that the per-vertex comparison is valid. To do that (where nick10 is subject data at one timepoint, and nick11 is subject data at another timepoint):
mri_surf2surf --hemi lh \ --srcsubject nick10 --srcsurfval thickness \ --src_type curv \ --trgsubject nick11 \ --trgsurfval nick10_thickness \ --trg_type curv
then convert the nick10_thickness file to ascii:
mris_convert -c lh.nick10_thickness \ lh.white lh.nick10_thickness.asc
then you can compare the data in lh.thickness.asc to lh.nick10_thickness.asc, although I can't comment on the statistical validity of doing such a comparison.
Nick
On Sun, 2007-05-06 at 23:41 -0500, David Perlman wrote:
Forgive me if I'm simply missing the obvious, but as far as I can tell, mri_surf2surf is not capable of writing output in *any* of the surface formats listed in the Freesurfer surface formats document on the wiki, except .w paint format. Also, mris_convert doesn't accept .w as input; so there's no way at all to get output from mri_surf2surf into ascii format?
I'm also confused about why mri_surf2surf only writes out in volume formats like analyze and mgh (other than .w). If there are surface versions of these filetypes, where can I find documentation about those other surface formats, since they're not in the existing surface formats document?
Actually, this is all extra confusing because the output of --help for mri_surf2surf conflicts with the documentation on the wiki. The wiki says output can be curv format; the --help says not. It doesn't seem to be possible. Also some of the options have different names in the two locations.
Just out of curiosity, why does it work like that? I'd think it would make more sense simply to have it write out in the standard surface formats (surface or curv or ascii)...
All I'm trying to do is to subtract one set of curv-format data from another. (I have cortical thickness measures for the same subjects at two different times, and I want to be able to see the changes for individual subjects.) I have successfully registered the time 1 data onto the time 2 surface, and I can visualize it overlaid no problem. But I am struggling to find a way to subtract the aligned data... which seems like it should be easy... which makes me think I'm missing something obvious, but I've been searching through documentation for hours. I can see how to do it with Matlab, using mri_surf2surf to generate .w format output and reading it into Matlab, but I was hoping there would be a more straightforward way...
Also, as an aside, the comments for read_wfile.m are actually the comments for write_wfile.m. -- -dave---------------------------------------------------------------- After all, it is not *that* inexpressible. -H.H. The Dalai Lama
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
David Perlman -
Nick Schmansky