Re: [HCP-Users] subdivide parcellation

[Harms, Michael]

I don't think we've had any discussions about releasing the Freesurfer outputs in their "native" FS directory structure. Indeed, it would be quite redundant to do so. cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: basile pinsard <basile.pins...@gmail.com> Date: Monday, March 17, 2014 9:51 AM To: Donna Dierker <do...@brainvis.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] subdivide parcellation Hi Donna, so you mean this is the files that will be in the next release? Because what I get from downloading preprocessed structural does not has this structure, here is a list for one subject: STRU/101915/T1w/101915_3T.csv STRU/101915/T1w/aparc.a2009s+aseg.nii.gz STRU/101915/T1w/aparc+aseg.nii.gz STRU/101915/T1w/BiasField_acpc_dc.nii.gz STRU/101915/T1w/brainmask_fs.nii.gz STRU/101915/T1w/fsaverage_LR32k STRU/101915/T1w/fsaverage_LR32k/101915.32k_fs_LR.wb.spec STRU/101915/T1w/fsaverage_LR32k/101915.L.inflated.32k_fs_LR.surf.gii STRU/101915/T1w/fsaverage_LR32k/101915.L.midthickness.32k_fs_LR.surf.gii STRU/101915/T1w/fsaverage_LR32k/101915.L.pial.32k_fs_LR.surf.gii STRU/101915/T1w/fsaverage_LR32k/101915.L.very_inflated.32k_fs_LR.surf.gii STRU/101915/T1w/fsaverage_LR32k/101915.L.white.32k_fs_LR.surf.gii STRU/101915/T1w/fsaverage_LR32k/101915.R.inflated.32k_fs_LR.surf.gii STRU/101915/T1w/fsaverage_LR32k/101915.R.midthickness.32k_fs_LR.surf.gii STRU/101915/T1w/fsaverage_LR32k/101915.R.pial.32k_fs_LR.surf.gii STRU/101915/T1w/fsaverage_LR32k/101915.R.very_inflated.32k_fs_LR.surf.gii STRU/101915/T1w/fsaverage_LR32k/101915.R.white.32k_fs_LR.surf.gii STRU/101915/T1w/Native STRU/101915/T1w/Native/101915.L.inflated.native.surf.gii STRU/101915/T1w/Native/101915.L.midthickness.native.surf.gii STRU/101915/T1w/Native/101915.L.pial.native.surf.gii STRU/101915/T1w/Native/101915.L.very_inflated.native.surf.gii STRU/101915/T1w/Native/101915.L.white.native.surf.gii STRU/101915/T1w/Native/101915.native.wb.spec STRU/101915/T1w/Native/101915.R.inflated.native.surf.gii STRU/101915/T1w/Native/101915.R.midthickness.native.surf.gii STRU/101915/T1w/Native/101915.R.pial.native.surf.gii STRU/101915/T1w/Native/101915.R.very_inflated.native.surf.gii STRU/101915/T1w/Native/101915.R.white.native.surf.gii STRU/101915/T1w/ribbon.nii.gz STRU/101915/T1w/T1w_acpc_dc.nii.gz STRU/101915/T1w/T1w_acpc_dc_restore_brain.nii.gz STRU/101915/T1w/T1w_acpc_dc_restore.nii.gz STRU/101915/T1w/T1wDividedByT2w.nii.gz STRU/101915/T1w/T1wDividedByT2w_ribbon.nii.gz STRU/101915/T1w/T2w_acpc_dc.nii.gz STRU/101915/T1w/T2w_acpc_dc_restore_brain.nii.gz STRU/101915/T1w/T2w_acpc_dc_restore.nii.gz STRU/101915/T1w/wmparc.nii.gz Thanks Basile On Mon, Mar 17, 2014 at 3:35 PM, Donna Dierker <do...@brainvis.wustl.edu> wrote: 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 <basile.pins...@gmail.com> 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 <markus.gschw...@gmail.com> 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 <basile.pins...@gmail.com>: > 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 > 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   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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