Re: [HCP-Users] subdivide parcellation

[Glasser, Matthew]

They would not necessarily be aligned with the other data either, given that they exist in their own 1mm RAS space, not the 0.7mm RPI spaces released by the HCP.   For this particular task, I would use: brainmappers@brainmappers-desktop1:~$ mris_make_face_parcellation  usage: mris_make_face_parcellation [options] <input surface> <ico file> <output annot> example: mris_make_face_parcellation lh.surf $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot   surf should be either:     sphere: units will be approximately equal size within subject but              not in correspondence across subjects     sphere.reg: units will be different sizes within subject but              in correspondence across subjects   Note: do not use inflated as was suggested by previous versions!     This generates a parcellation based on which icosahedral face each vertex maps to. Options:    -ctab colortable.txt Most FreeSurfer binaries work with GIFTI files now (the .label.gii files are equivalent to annot), but sometimes they have "hidden" inputs that may be hard coded to old formats and directory structures.  If this is the case, they will throw a descriptive error message and you may need to use mris_convert to convert some GIFTI file to be whatever the binary is looking for.   Peace, Matt. From: <Harms>, Michael <mha...@wustl.edu> Date: Monday, March 17, 2014 10:04 AM To: basile pinsard <basile.pins...@gmail.com>, Donna Dierker <do...@brainvis.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] subdivide parcellation 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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