Re: [Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)
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-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" 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 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 >> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)
Hi Daniel I don't think we can help you with why Surf Ice is failing (at least I can't). What are the features that freeview doesn't have? I'll leave question 2 for Doug cheers Bruce On Wed, 23 Jan 2019, Daniel Leopold wrote: External Email - Use Caution Hello FS experts and enthusiasts, Thus far, I have used mri_concat to make 4D files of subjects' lh.thickness.fwhm15.fsaverage.mgh files to be used as input for palm. The results maps are of the .mgz format. I can convert these to .nii using mri_convert in order to use fslmaths or fslstats. My dilemma is that I'd like to use another viewing package for the palm results (i.e., Surf Ice) because of its features and some quirks I've encountered while loading results in Freeview. Surf Ice accepts a number of formats (https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Supported_Formats), including Freesurfer's .asc, .srf, .curv, .gcs, .pial, and .w (among many others), but I have yet to successfully convert these .mgz maps to a readable format. Surf Ice can read .nii, but loading my mri_converted .nii files results in a uniform surface with 0 at all vertices. Thus, I have two questions: 1) Can you think of a means to convert these surface "volumes" (.mgh/.mgz) to a desired format that can be read by Surf Ice? I've attempted mri_vol2surf, mri_surf2surf, and mris_convert, but cannot find an appropriate format/get things to work. In case it's helpful, readable formats are: 2) My alternative idea would be to instead use mri_concat on subjects' lh.thickness files and later apply fwhm smoothing. Would this approach be feasible? I could test whether pre-palm smoothed and post-palm smoothed results are equivalent, but I'm afraid that the variable dimensions of subjects' native thickness files would cause problems either with palm or when later trying to view the group-level results. Version information: Recon-all run with FreeSurfer 5.3.0 FSL 5.0.8 palm alpha112 Thank you in advance for any suggestions, and please let me know if any additional information would be helpful. With gratitude, Dan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)
External Email - Use Caution Hello FS experts and enthusiasts, Thus far, I have used mri_concat to make 4D files of subjects' lh.thickness.fwhm15.fsaverage.mgh files to be used as input for palm. The results maps are of the .mgz format. I can convert these to .nii using mri_convert in order to use fslmaths or fslstats. My dilemma is that I'd like to use another viewing package for the palm results (i.e., Surf Ice) because of its features and some quirks I've encountered while loading results in Freeview. Surf Ice accepts a number of formats ( https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Supported_Formats), including Freesurfer's .asc, .srf, .curv, .gcs, .pial, and .w (among *many* others), but I have yet to successfully convert these .mgz maps to a readable format. Surf Ice can read .nii, but loading my mri_converted .nii files results in a uniform surface with 0 at all vertices. Thus, I have two questions: 1) Can you think of a means to convert these surface "volumes" (.mgh/.mgz) to a desired format that can be read by Surf Ice? I've attempted mri_vol2surf, mri_surf2surf, and mris_convert, but cannot find an appropriate format/get things to work. In case it's helpful, readable formats are: 2) My alternative idea would be to instead use mri_concat on subjects' lh.thickness files and later apply fwhm smoothing. Would this approach be feasible? I could test whether pre-palm smoothed and post-palm smoothed results are equivalent, but I'm afraid that the variable dimensions of subjects' native thickness files would cause problems either with palm or when later trying to view the group-level results. Version information: Recon-all run with FreeSurfer 5.3.0 FSL 5.0.8 palm alpha112 Thank you in advance for any suggestions, and please let me know if any additional information would be helpful. With gratitude, Dan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
