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Hi Bruce,
Chris Rorden informed me that Surfice previously assumed that MGZ/MGH files were voxelwise images used to surface-paint a mesh. Anderson's palm, however, uses the format as a one-to-one correspondence with the vertices (i.e., data-per-vertex). Chris' newest/upcoming version of Surfice automatically detects this data-per-vertex format and can load the files appropriately.
The main feature that freeview lacks is the ability to display multiple overlays/sets of palm results at once. My initial approach was to convert the .mgz palm outputs into .nii so that I could use fslmaths to combine results, but (apparently) NIFTI handles a maximum of 65,535 voxels in any one dimension, which is why Chris thought Anderson used MGH, which allows billions of vertices (32-bit).
So, Surfice can now load the palm .mgz outputs onto ?h.inflated, .pial, and .curv surfaces, but I'm now wondering if mgh/mgz overlays be be loaded on top of other background meshes (such as BrainMesh_ICBM152 or mni2fs meshes that are provided with Surfice). I've emailed Darren Price because I'm essentially looking for the inverse transform of his mni2fs package (i.e., fs2mni), but I was wondering if you or Doug have encountered this question or similar requests to convert freesurfer to mni surfaces/meshes before? I'm familiar with the Freesurfer Coordinate Systems info, but I don't know how I might generalize the RAS to MNI152 point conversion to an entire surface.
Thank you again for your suggestions and help! Dan
Hi Dan
sorry, I'm not really sure what you are asking. Doug implemented a work-around for nifti in which it breaks up the number of vertices into multiple dimensions (to get around the 16-bit dimensions in nifti, which was a crazy design decision). freeview detects this and displays them appropriately
cheers Bruce
On Wed, 30 Jan 2019, Daniel Leopold wrote:
External Email - Use Caution
Hi Bruce,
Chris Rorden informed me that Surfice previously assumed that MGZ/MGH files were voxelwise images used to surface-paint a mesh. Anderson's palm, however, uses the format as a one-to-one correspondence with the vertices (i.e., data-per-vertex). Chris' newest/upcoming version of Surfice automatically detects this data-per-vertex format and can load the files appropriately.
The main feature that freeview lacks is the ability to display multiple overlays/sets of palm results at once. My initial approach was to convert the .mgz palm outputs into .nii so that I could use fslmaths to combine results, but (apparently) NIFTI handles a maximum of 65,535 voxels in any one dimension, which is why Chris thought Anderson used MGH, which allows billions of vertices (32-bit).
So, Surfice can now load the palm .mgz outputs onto ?h.inflated, .pial, and .curv surfaces, but I'm now wondering if mgh/mgz overlays be be loaded on top of other background meshes (such as BrainMesh_ICBM152 or mni2fs meshes that are provided with Surfice). I've emailed Darren Price because I'm essentially looking for the inverse transform of his mni2fs package (i.e., fs2mni), but I was wondering if you or Doug have encountered this question or similar requests to convert freesurfer to mni surfaces/meshes before? I'm familiar with the Freesurfer Coordinate Systems info, but I don't know how I might generalize the RAS to MNI152 point conversion to an entire surface.
Thank you again for your suggestions and help! Dan
External Email - Use Caution
Isn¹t this what GIFTI is for? PALM and FreeSurfer can use GIFTI.
Matt.
On 1/30/19, 9:17 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Dan
sorry, I'm not really sure what you are asking. Doug implemented a work-around for nifti in which it breaks up the number of vertices into multiple dimensions (to get around the 16-bit dimensions in nifti, which was a crazy design decision). freeview detects this and displays them appropriately
cheers Bruce
On Wed, 30 Jan 2019, Daniel Leopold wrote:
External Email - Use CautionHi Bruce,
Chris Rorden informed me that Surfice previously assumed that MGZ/MGH files were voxelwise images used to surface-paint a mesh. Anderson's palm, however, uses the format as a one-to-one correspondence with the vertices (i.e., data-per-vertex). Chris' newest/upcoming version of Surfice automatically detects this data-per-vertex format and can load the files appropriately.
The main feature that freeview lacks is the ability to display multiple overlays/sets of palm results at once. My initial approach was to convert the .mgz palm outputs into .nii so that I could use fslmaths to combine results, but (apparently) NIFTI handles a maximum of 65,535 voxels in any one dimension, which is why Chris thought Anderson used MGH, which allows billions of vertices (32-bit).
So, Surfice can now load the palm .mgz outputs onto ?h.inflated, .pial, and .curv surfaces, but I'm now wondering if mgh/mgz overlays be be loaded on top of other background meshes (such as BrainMesh_ICBM152 or mni2fs meshes that are provided with Surfice). I've emailed Darren Price because I'm essentially looking for the inverse transform of his mni2fs package (i.e., fs2mni), but I was wondering if you or Doug have encountered this question or similar requests to convert freesurfer to mni surfaces/meshes before? I'm familiar with the Freesurfer Coordinate Systems info, but I don't know how I might generalize the RAS to MNI152 point conversion to an entire surface.
Thank you again for your suggestions and help! Dan
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