Re: [HCP-Users] gifti labels to volume

[Glasser, Matthew]

I’m a bit surprised at these issues with probtrackx (I’ve not had problems with stop surfaces for example), perhaps you should ask for help/clarification on the FSL list?  It certainly would seem to be the path of least resistance/most accurate to use FSL for tractography since it already works with HCP data (and in the future we will be providing fiber orientation results for FSL as well).  Also if there are important features missing, I think we would all like to know about that.   Peace, Matt. From: basile pinsard <basile.pins...@gmail.com> Date: Thursday, June 5, 2014 at 7:42 AM To: Donna Dierker <do...@brainvis.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: 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 <do...@brainvis.wustl.edu> 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 <tsc...@mst.edu> 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 <basile.pins...@gmail.com> 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   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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users