Hi basile, Note that I'm looking at the structure for the data that is about to come out, but I see the Freesurfer original directory structure here:
T1w/106016 T1w/106016/label T1w/106016/mri T1w/106016/mri/orig T1w/106016/mri/transforms T1w/106016/scripts T1w/106016/stats T1w/106016/surf T1w/106016/touch Donna On Mar 15, 2014, at 5:50 PM, basile pinsard <[email protected]> wrote: > Many thanks for the answers. > > @Mark: this seems an interesting option if it enables to overcome the fact > that mris_divide_parcellation won't work on gifti and needs freesurfer > original subject directory structure. I will need to adapt it to search for > the files in hcp structure and handle gifti files though. > > @Markus : The only limitation I see for using cmtk Lausanne parcellation on > hcp data is the fact it requires regular freesurfer outputs/structure to run > it relying on freesurfer binaries. I think they are not contained in the hcp > release and this certainly imply converting gitfti back to freesurfer format? > Or rerunning sub-optimally freesurfer (without .7mm optimization etc). > > Best, > basile > > > > On Sat, Mar 15, 2014 at 10:33 PM, Markus Gschwind <[email protected]> > wrote: > Hi! > > You might be interested in the parcellation tool form connectomemapper in > nipype > http://nipy.org/nipype/0.6/interfaces/generated/nipype.interfaces.cmtk.parcellation.html > > or the connectomemapper itself: > http://www.cmtk.org/mapper/stages.html#parcellation > > This is the tool that created the multi-parcellation presented in > http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060159 > > Best, > Markus > > > 2014-03-14 20:10 GMT+01:00 basile pinsard <[email protected]>: > Hi HCP experts, > > I am trying to subdivide the aparc.a2009s parcellation (for cortex only, > maybe cerebellum too) to get more homogeneous sized parcels (preserving > connectivity) to perform connectivity study at the subject level from > densetimeseries, I can think of many ways to do this but none is that simple > to carry out. > Is there a command that would be appropriate in wb_command utility? > What do you think would be the best way to proceed? > Is it possible to simply map a surface parcellation from fsaverage to a > subject's fsaverage32k space? > > Thanks > Best regards. > > basile > _______________________________________________ > > > 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
