Hi Eran, No easy answers leap to mind, but a few questions/thoughts:
* You imported the surface, but were unable to import the parcels? Or the link between the two wasn't evident? The vertex index/number is the link between the two. The surf.gii has the x,y,z coords (and it matters whether you choose white, midthickness, or pial), and the label file has the vertex-parcel assignment. Depending on your reader/conversion programs, it might be easier to convert from cifti to gifti to import into matlab, though there is a toolbox for reading cifti in matlab. * This sort of thing was trivial in caret_command (surface-region-of-interest-selection and surface-roi-statistical-report), but I can't find equivalent functionality in wb_command, after looking at the wb_command list commands output and searching the full help output for words like report, information, and coordinate. Maybe Matt or Tim can help me find it, if it is there. * I confess I wonder what your broader goals are, because I look at parcellations like these: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011 … and I think some of those parcels are pretty big/extended -- elongated and subject to considerable gyrification. A center of gravity seems less useful to me in this context, though for the subcortical structures it seems more useful. Those are the thoughts that come to mind. Donna On Jul 17, 2015, at 2:30 PM, "Dayan, Eran (NIH/NINDS) [F]" <eran.da...@nih.gov> wrote: > Hi Donna > > Just to follow up on my previous question. I am indeed trying to compute > center of gravity (in MNI or talairach) for all cortical and subcortical > parcels from which volume measurements were extracted. I was able to import > the various surf.gii files in MATLAB, but it isn't helping me much as I can't > register the actual parcels onto this imported image and therefore can't > compute what I need. Are you aware, by any chance, of any other way this can > be done? > > > Many thanks > > E. > > -----Original Message----- > From: Dayan, Eran (NIH/NINDS) [F] > Sent: Wednesday, July 01, 2015 12:51 PM > To: 'Donna Dierker' > Subject: RE: [HCP-Users] Freesurfer parcellation - list of coordinates > > Hi Donna > > Thanks! I will have a look right away. Yes, the idea is to compute center of > gravity. But if all coordinates are available for each parcel then it's > pretty easy (e.g., through MATLAB) > > Best > > Eran > > -----Original Message----- > From: Donna Dierker [mailto:do...@brainvis.wustl.edu] > Sent: Wednesday, July 01, 2015 12:17 PM > To: Dayan, Eran (NIH/NINDS) [F] > Cc: hcp-users@humanconnectome.org > Subject: Re: [HCP-Users] Freesurfer parcellation - list of coordinates > > Hi Eran, > > An HCP subject's MNINonLinear subdirectory has files like: > > *.surf.gii - vertex coordinate and neighbor relationships *aparc*dlabel.nii - > vertex parcel assignments > > So for any vertex, its coords are in *surf.gii and its parcels are in > *aparc*dlabel.nii. > > This is for the cortex. For the subcortical structures, you have > aparc+aseg.nii.gz. > > Are you trying to compute a center of gravity for the parcels which span > multiple vertices/voxels? > > Donna > > > On Jun 30, 2015, at 12:20 PM, "Dayan, Eran (NIH/NINDS) [F]" > <eran.da...@nih.gov> wrote: > >> >> Was wondering if at some point along the Freesurfer pipeline, the >> (MNI/Talairach) coordinates of the parcellated cortical and subcortical >> structures were saved? If so, how can these be accessed? >> >> Many thanks! >> >> Eran > > _______________________________________________ > 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
