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 <[email protected]> > 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 <[email protected]> > Date: Friday, October 25, 2013 12:40 AM > To: Matt Glasser <[email protected]> > Cc: "[email protected]" <[email protected]> > 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" <[email protected]> > 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 <[email protected]> >> Date: Thursday, October 24, 2013 7:05 PM >> To: "[email protected]" <[email protected]> >> 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 >> [email protected] >> 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. 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. >> > > > > 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. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
