I think I must be misunderstanding something about the way mri_surf2surf works. I thought it was supposed to resample onto the target mesh, which I would think would mean that resampling two different data files onto the same target mesh would give outputs with the same numbers of nodes. But when I do this and then read the resampled data into Matlab, the nodes do not match up. Here are the commands I used:
mri_surf2surf --srcsubject sp01t7 --hemi lh --srcsurfval thickness -- src_type curv --trgsubject sp01MULTt1 --trgsurfval ../../sp01MULTt1/ surf/t7tot1-lh.thickness.w --trg_type w
mri_surf2surf --srcsubject sp01t6 --hemi lh --srcsurfval thickness -- src_type curv --trgsubject sp01MULTt1 --trgsurfval ../../sp01MULTt1/ surf/t6tot1-lh.thickness.w --trg_type w
And here's what I see in Matlab:
[vt6to1,ft6to1]=read_wfile('t6tot1-lh.thickness.w'); [vt7to1,ft7to1]=read_wfile('t7tot1-lh.thickness.w'); size(vt6to1)
ans =
124463 1
size(vt7to1)
ans =
124134 1
What am I missing here?
-- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe
This is a quirk of the wfile format (just one of the reasons to move away from it:). The wfile is "compressed" in that values that are 0 are not represented. The indices of the values that are there are given in the 2nd output arugment to read_wfile. But it is much easier to just:
mri_surf2surf --srcsubject sp01t7 --hemi lh --srcsurfval thickness --src_type curv --trgsubject sp01MULTt1 --trgsurfval ../../sp01MULTt1/surf/t7tot1-lh.thickness.mgh
doug
On Mon, 7 May 2007, David Perlman wrote:
I think I must be misunderstanding something about the way mri_surf2surf works. I thought it was supposed to resample onto the target mesh, which I would think would mean that resampling two different data files onto the same target mesh would give outputs with the same numbers of nodes. But when I do this and then read the resampled data into Matlab, the nodes do not match up. Here are the commands I used:
mri_surf2surf --srcsubject sp01t7 --hemi lh --srcsurfval thickness --src_type curv --trgsubject sp01MULTt1 --trgsurfval ../../sp01MULTt1/ surf/t7tot1-lh.thickness.w --trg_type w
mri_surf2surf --srcsubject sp01t6 --hemi lh --srcsurfval thickness --src_type curv --trgsubject sp01MULTt1 --trgsurfval ../../sp01MULTt1/ surf/t6tot1-lh.thickness.w --trg_type w
And here's what I see in Matlab:
[vt6to1,ft6to1]=read_wfile('t6tot1-lh.thickness.w'); [vt7to1,ft7to1]=read_wfile('t7tot1-lh.thickness.w'); size(vt6to1)
ans =
124463 1size(vt7to1)
ans =
124134 1What am I missing here?
-- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hmm, and then in Matlab it would be:
datastruct=MRIread('t7tot1-lh.thickness.mgh');
datavol=datastruct.vol;
data=datavol(:,1,1,1);
except that it "might be reshaped" so if I want to read surface data in mgh format I have to check for reshaping and then un-reshape it as necessary... there really is no easier way? Or is there a Matlab function I'm missing that reads mgh surface data automatically like all the other readxxx.m functions do for the older formats?
I suppose if there isn't, I'll just have to write read_mgh_surface.m and send it to you. :)
On May 7, 2007, at 11:49 PM, Doug Greve wrote:
This is a quirk of the wfile format (just one of the reasons to move away from it:). The wfile is "compressed" in that values that are 0 are not represented. The indices of the values that are there are given in the 2nd output arugment to read_wfile. But it is much easier to just:
mri_surf2surf --srcsubject sp01t7 --hemi lh --srcsurfval thickness --src_type curv --trgsubject sp01MULTt1 -- trgsurfval ../../sp01MULTt1/surf/t7tot1-lh.thickness.mgh
-- -dave---------------------------------------------------------------- After all, it is not *that* inexpressible. -H.H. The Dalai Lama
If you add --noreshape to surf2surf, then it won't reshape it:
mri_surf2surf --srcsubject sp01t7 --hemi lh --srcsurfval thickness --src_type curv --trgsubject sp01MULTt1 --trgsurfval ../../sp01MULTt1/surf/t7tot1-lh.thickness.mgh --noreshape
Just don't use analyze or nifti (and blame them for reshaping:).
doug
On Mon, 7 May 2007, David Perlman wrote:
Hmm, and then in Matlab it would be:
datastruct=MRIread('t7tot1-lh.thickness.mgh');
datavol=datastruct.vol;
data=datavol(:,1,1,1);
except that it "might be reshaped" so if I want to read surface data in mgh format I have to check for reshaping and then un-reshape it as necessary... there really is no easier way? Or is there a Matlab function I'm missing that reads mgh surface data automatically like all the other readxxx.m functions do for the older formats?
I suppose if there isn't, I'll just have to write read_mgh_surface.m and send it to you. :)
On May 7, 2007, at 11:49 PM, Doug Greve wrote:
This is a quirk of the wfile format (just one of the reasons to move away from it:). The wfile is "compressed" in that values that are 0 are not represented. The indices of the values that are there are given in the 2nd output arugment to read_wfile. But it is much easier to just:
mri_surf2surf --srcsubject sp01t7 --hemi lh --srcsurfval thickness --src_type curv --trgsubject sp01MULTt1 -- trgsurfval ../../sp01MULTt1/surf/t7tot1-lh.thickness.mgh
-- -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
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David Perlman -
Doug Greve