Hi - I actually sent this a couple of weeks back, but only just noticed it was bounced back because I used the wrong address.
Happy new year!
Date: Sat, 14 Dec 2013 09:57:27 +0000 Subject: import from CARET Hi -
If one has a surface that is aligned to a volume in CARET, is it possible (or rather, is there a general procedure) to export the volume and the surface into freesurfer?
The volume in CARET won't be conformed. It's header will define the origin such that CARET interprets a specific voxel/coordinate as the anterior commisure.
The surface will be aligned to the volume in the sense that it's co-ordinates work with respect to that header/origin.
What I need to do is run mri_convert -c to conform the volume, and then convert the surface to freesurfer format in such a way that it's now aligned to the conformed volume in freesurfer.
Then I'd do some stuff (refine the surface) in freesurfer, and export the surface back to CARET.
That's the general issue. Details include: the surface will need to be transformed so that it appears to freesurfer to be 1mm data, and the volume will have it's header changed so that it claims 1mm voxels (the data is higher resolution than 1mm). that should be fine.
Also, there will be no ?h.orig surface, and the mesh is arbitrary wrt the MRI data (not derived from it in any way). I don't know if that matters.
The problem can be considered as finding the inverse of Van Essen's Freesurfer to F99 pipeline. Pretty much.
It's some scaling, translating, conforming and format conversions.
connectome workbench, FS, CARET, FSL, MATLAB whatever are all relevant/involved tools
hope can help
Colin Reveley
Hi Colin, I'm not familiar with CARET, and I don't think that any of the other FS developers are either. Maybe contact the wash u guys? doug
On 12/27/13 12:54 PM, Colin Reveley wrote:
Hi - I actually sent this a couple of weeks back, but only just noticed it was bounced back because I used the wrong address.
Happy new year!
Date: Sat, 14 Dec 2013 09:57:27 +0000 Subject: import from CARET Hi -
If one has a surface that is aligned to a volume in CARET, is it possible (or rather, is there a general procedure) to export the volume and the surface into freesurfer?
The volume in CARET won't be conformed. It's header will define the origin such that CARET interprets a specific voxel/coordinate as the anterior commisure.
The surface will be aligned to the volume in the sense that it's co-ordinates work with respect to that header/origin.
What I need to do is run mri_convert -c to conform the volume, and then convert the surface to freesurfer format in such a way that it's now aligned to the conformed volume in freesurfer.
Then I'd do some stuff (refine the surface) in freesurfer, and export the surface back to CARET.
That's the general issue. Details include: the surface will need to be transformed so that it appears to freesurfer to be 1mm data, and the volume will have it's header changed so that it claims 1mm voxels (the data is higher resolution than 1mm). that should be fine.
Also, there will be no ?h.orig surface, and the mesh is arbitrary wrt the MRI data (not derived from it in any way). I don't know if that matters.
The problem can be considered as finding the inverse of Van Essen's Freesurfer to F99 pipeline. Pretty much.
It's some scaling, translating, conforming and format conversions.
connectome workbench, FS, CARET, FSL, MATLAB whatever are all relevant/involved tools
hope can help
Colin Reveley
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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Colin Reveley -
Douglas Greve