Re: [HCP-Users] Projecting diffusion MRI indices to gii surfaces

[Glasser, Matthew]

Yes you can use wb_command -surface-cortex-layer.  Note that this corrects these mid surfaces for the effects of folding (so that they properly follow the cortical layers).  If you want regularly spaced surfaces, you can use wb_command -surface-average (averaging white and pial surfaces produces a midthickness at 0.5, averaging midthickness and white produces a 0.25, etc…). Peace, Matt. From: Arash Nazeri <arashnaz...@gmail.com> Date: Saturday, October 26, 2013 9:31 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Projecting diffusion MRI indices to gii surfaces Thank you very much. It all worked just fine. Is there a way to generate surfaces at various depths of cortex (e.g. 0.4 of the cortical thickness)? If so, is it sound to use two near mid-cortical ( e.g. at 0.4 and 0.6 depth) and use ribbon constrained? Cheers, Arash On Fri, Oct 25, 2013 at 12:27 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: Unfortunately we didn't port that outlier feature over to Connectome Workbench after we got substantially better myelin maps with the high resolution HCP data (though the myelin mapping volume to surface mapping algorithm is ported over).  You could probably do something similar in several steps by thresholding the outliers  using wb_command -metric-math and then using wb_command -metric-dilate without the -nearest option.  Tim might have further thoughts on this.   HCP works on the FS_LR surface atlas, which is related to fsaverage (in fact, it is a version of fsaverage with left/right vertex correspondence).  If you map your data onto the native mesh, you can use wb_command -metric-resample with ${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.${Hemisphere}.sphere.reg.reg_LR.native.surf.gii as the current-sphere and ${StudyFolder}/${Subject}/MNINonLinear/${Subject}.${Hemisphere}.sphere.164k_fs_LR.surf.gii as the new-sphere.  We recommend using the ADAP_BARY_AREA resampling method and the area surfs (native mesh midthickness and 164k_fs_LR midthickness).  If you really need to get to fsaverage itself, you'll need to make a GIFTI version of that sphere and you can use wb_command -metric-resample with .sphere.reg (no .reg_LR). Matlab GIFTI toolbox works fine for me (look in the .cdata structure).  Do you have the latest version of that? Peace, Matt. From: Arash Nazeri <arashnaz...@gmail.com> Date: Friday, October 25, 2013 12:40 AM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Projecting diffusion MRI indices to gii surfaces Matt, Thank you very much for your prompt response.  Is it also possible to find outliers and replace them with the local average as, caret does for myelin mapping? Also I'm not familiar with the workbench software, could this diffusion data func.gii be transformed to the MNI fs average surface, using the workbench?  And one last question, is that the MATLAB gifti toolbox doesn't seem to take care of func.gii,files and it only imports the vertices and faces. How could the assigned values also be imported to the MATLAB? Sorry for the long list of questions Cheers Arash On Oct 24, 2013, at 9:01 PM, "Glasser, Matthew" <glass...@wusm.wustl.edu> wrote: Yes use the native surface files in ${StudyFolder}/${Subject}/T1w/Native for mapping diffusion data to the surface.  I would use  wb_command -volume-to-surface-mapping.  If you want to map the data to one surface like the midthickness, you can use -cubic.  If you wanted to map it from the whole grey matter ribbon, you can use -ribbon-constrained.  For labels/masks, you would use -enclosing. Peace, Matt. From: Arash Nazeri <arashnaz...@gmail.com> Date: Thursday, October 24, 2013 7:05 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Projecting diffusion MRI indices to gii surfaces Dear all, I want to assign values to mid-cortical surface gifti file from the surrounding cortical voxels of a diffusion map (e.g. FA map), to create a .func.gii file.  Could this be carried out using mri_vol2surf with the files provided from HCP?  Should this be carried out using native surface files in the native space? Cheers, Arash _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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