Hi Saad, great, many thanks
cheers basile On Thu, Jun 5, 2014 at 6:45 PM, Saad Jbabdi <[email protected]> wrote: > Hi Basile et al. > > We will make this three-vertex count optional in the future, as I agree > that it complicates interpretation of matrix1/3 output. > > Cheers > Saad > > > > On 5 Jun 2014, at 12:30, Glasser, Matthew <[email protected]> > wrote: > > You could do that but because white is the counting surface and pial is > the stopping surface it is unlikely to be necessary. > > So basically you don’t like the fact that when a surface triangle is > hit, all three vertices counts are incremented instead of the nearest > vertex? I suppose that’s not such a good idea if one were connection > strengths of different kinds of structures. I’ll ask them about it this > afternoon. > > Peace, > > Matt. > > From: basile pinsard <[email protected]> > Date: Thursday, June 5, 2014 at 11:42 AM > To: Matt Glasser <[email protected]> > Cc: Donna Dierker <[email protected]>, " > [email protected]" <[email protected]> > Subject: Re: [HCP-Users] gifti labels to volume > > ok, do you have applied dilation to the mask before inverting it? can't > there be side effect between aliased volume mask and wm/gm surfaces? > However I wonder if in the case it misses the surface for stopping > condition and crosses over if the fiber is counted as endpoint in the > matrix... > > the second point is about normalization of the matrix when summing over > regions of interest (to get some kind of more quantitative value). When a > fiber hits a triangle all of the 3 vertex entries in the matrices (let say > rows) to the other endpoint of the fiber have their count increased of 1. > so it will count each fiber either 4*3/2= 6 times if one end is on a vertex > and the other in a volume ROI or 6*5/2=15 times if both endpoints are > surfaces. So dividing by this numbers the fibers count when summing over > ROIS is necessary to get sensible results. However the diagonal value will > carry over-estimated self-connecting fibers as pairs of vertices in the > same triangle have their count increment each time a fiber hits this > triangle. This can be filtered if you remove every matrix entry of > neighboring vertices on the surface. > > hope this is clear enough, you can also see this thread here: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;a98283e4.1405 > > cheers > > basile > > > On Thu, Jun 5, 2014 at 12:26 PM, Glasser, Matthew <[email protected] > > wrote: > >> I’ve used the 32k mesh. Also I restrict the tracking mask not to allow >> stuff outside the brain (inverse of HCP distributed wmparc file minus the >> ventricles), so even a few fibers missed don’t go far (--mask= option). >> >> Not sure I understand your other point. Can you have another try at >> explaining it? >> >> From: basile pinsard <[email protected]> >> Date: Thursday, June 5, 2014 at 11:19 AM >> To: Matt Glasser <[email protected]> >> Cc: Donna Dierker <[email protected]>, " >> [email protected]" <[email protected]> >> >> Subject: Re: [HCP-Users] gifti labels to volume >> >> Hi Matt, >> >> Even if it is marginal a certain number of fibers are in the cortical and >> ROIs gray matter as assessed by fdt_paths.nii, I think I already >> mentioned this to Saad on fsl list. >> Have you been using the fsaverage32k surface as stop/targets or the full >> resolution (which I believe would produce huge matrix compared to the >> already huge matrix when using fsaverage32k) ? >> >> Also I had a hard time to understand that for each fiber terminating on >> surfaces at it's endpoints all combinatorial pair of vertices of >> triangles which are hit are incremented. >> >> Cheers >> >> basile >> >> >> >> On Thu, Jun 5, 2014 at 9:45 AM, Glasser, Matthew <[email protected] >> > wrote: >> >>> 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 <[email protected]> >>> Date: Thursday, June 5, 2014 at 7:42 AM >>> To: Donna Dierker <[email protected]> >>> Cc: "[email protected]" <[email protected]> >>> 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 <[email protected]> >>> 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 <[email protected]> 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 < >>>> [email protected]> 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 >>>> > [email protected] >>>> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> > >>>> > >>>> > _______________________________________________ >>>> > HCP-Users mailing list >>>> > [email protected] >>>> > 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 >>> [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. >>> >> >> >> >> -- >> 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 >> >> >> ------------------------------ >> 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. >> > > > > -- > 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 > > > ------------------------------ > 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 > > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > (+44)1865-222466 (fax 717) > www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi > > -- 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
