Re: [HCP-Users] gifti labels to volume
Many thanks for the answers @Timothy I know that probtrackx2 support surfaces but I did not manage to make it work without hectic results (fiber crossing the surfaces used as stop, combinatorial counting of endpoints ... ), even if FSL seems the most able to process multi-shell data. @Donna I already tried the caret_command method but got stuck to converting the gifti scalars to a metric/paint format, I will give it a try with the command you mentioned, but still this implies a lot of conversion steps. However I wrote a python function that for each voxel in the cortical ribbon finds the closest vertex on the surface and assigns the latter's label,. The voxels which are close to the surface (white) should be properly assigned the right label which is ok for me as I am using this as target for tractography. Cheers basile On Thu, Jun 5, 2014 at 3:45 AM, Donna Dierker wrote: > As far as I know, caret5's multi-fiducial mapping is volume->surface > rahter than surface->volume. > > The caret_command method works, but you'll need to convert HCP surf.gii -> > caret5 coord/topo (caret_command -file-convert -sc …). And your label.gii > or func.gii will need to be converted, too (caret_command -file-convert > -format-convert BINARY …). > > > On Jun 4, 2014, at 7:22 PM, Timothy Coalson wrote: > > > Workbench currently doesn't have a way to do that. caret5 has a way to > do this (caret_command -surface-to-volume, and there is another method > called multi-fiducial mapping, though I'm not sure how to invoke it), > though you may need to do some file conversion. > > > > On a side note, FSL's probtrackx does support surface data, and is > generally what we advocate for tractography. > > > > Tim > > > > > > > > On Mon, Jun 2, 2014 at 8:50 AM, basile pinsard > wrote: > > Hi hcp experts, > > > > I was wondering if anybody knew a way to map back to volume the values > in a surface gifti from HCP data. The main interest is to create ROIs on > the surface using this topological constraint and then send it back to > volume for let say a tractography software which does not support surface. > > > > mri_surf2vol won't work as it requires the freesurfer structure (which > can certainly be restored by converting all the HCP files). > > > > Many thanks > > > > -- > > Basile Pinsard > > PhD candidate > > Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne > Universités, UPMC, INSERM, CNRS > > Unité de Neuroimagerie Fonctionnelle, CRIUGM, Université de Montréal > > ___ > > HCP-Users mailing list > > HCP-Users@humanconnectome.org > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > > ___ > > HCP-Users mailing list > > HCP-Users@humanconnectome.org > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > -- Basile Pinsard *PhD candidate* Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS Unité de Neuroimagerie Fonctionnelle, CRIUGM, Université de Montréal ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] gifti labels to volume
As far as I know, caret5's multi-fiducial mapping is volume->surface rahter than surface->volume. The caret_command method works, but you'll need to convert HCP surf.gii -> caret5 coord/topo (caret_command -file-convert -sc …). And your label.gii or func.gii will need to be converted, too (caret_command -file-convert -format-convert BINARY …). On Jun 4, 2014, at 7:22 PM, Timothy Coalson wrote: > Workbench currently doesn't have a way to do that. caret5 has a way to do > this (caret_command -surface-to-volume, and there is another method called > multi-fiducial mapping, though I'm not sure how to invoke it), though you may > need to do some file conversion. > > On a side note, FSL's probtrackx does support surface data, and is generally > what we advocate for tractography. > > Tim > > > > On Mon, Jun 2, 2014 at 8:50 AM, basile pinsard > wrote: > Hi hcp experts, > > I was wondering if anybody knew a way to map back to volume the values in a > surface gifti from HCP data. The main interest is to create ROIs on the > surface using this topological constraint and then send it back to volume for > let say a tractography software which does not support surface. > > mri_surf2vol won't work as it requires the freesurfer structure (which can > certainly be restored by converting all the HCP files). > > Many thanks > > -- > Basile Pinsard > PhD candidate > Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne > Universités, UPMC, INSERM, CNRS > Unité de Neuroimagerie Fonctionnelle, CRIUGM, Université de Montréal > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Brain Connectivity Matrices
I believe we don't include those in the releases, because dense connectome files are very large (~30GB each). You should be able to generate them by running wb_command -cifti-correlate on a subject's rfMRI dtseries file. Tim On Tue, Jun 3, 2014 at 5:55 PM, Ommen, Jurgen wrote: > Hello everyone, > > > > I’m working on graph theoretic analysis of the human’s brain network. > After studying the documentation of the Q3 release, I’ve only found group > average dense connectome files so far. > > > > I’d like to know if there are any connectivity matrices available for > individual subjects with which I could generate the corresponding > connectome networks. Do you provide this kind of data? Where could I find > it? > > And if not, do you plan to include it in future releases? > > > > > > Thanks for your help in advance and my best regards, > > Jürgen > > > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] gifti labels to volume
Workbench currently doesn't have a way to do that. caret5 has a way to do this (caret_command -surface-to-volume, and there is another method called multi-fiducial mapping, though I'm not sure how to invoke it), though you may need to do some file conversion. On a side note, FSL's probtrackx does support surface data, and is generally what we advocate for tractography. Tim On Mon, Jun 2, 2014 at 8:50 AM, basile pinsard wrote: > Hi hcp experts, > > I was wondering if anybody knew a way to map back to volume the values in > a surface gifti from HCP data. The main interest is to create ROIs on the > surface using this topological constraint and then send it back to volume > for let say a tractography software which does not support surface. > > mri_surf2vol won't work as it requires the freesurfer structure (which can > certainly be restored by converting all the HCP files). > > Many thanks > > -- > Basile Pinsard > > *PhD candidate* > Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne > Universités, UPMC, INSERM, CNRS > Unité de Neuroimagerie Fonctionnelle, CRIUGM, Université de Montréal > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
