for those interested I just wrote a small dirty function: https://github.com/bpinsard/misc/blob/master/split_labels_hcp.py which splits the labels using the principal axis, but I changed the MNE-tools original code to split in regions with somewhat even number of vertices in each, which must be someway a proxy for the surface of cortex. It seems not to be the case in the original code, which splits at regular space along axis (like chopping a carrot), but I cannot assert as I didn't tested it.
a small example is provided, but I do not save the resulting array as gifti format is somewhat obscure to me. use at you own risks cheers. basile On Mon, Mar 17, 2014 at 5:24 PM, Glasser, Matthew <[email protected]>wrote: > My understanding is that is what this command does (or can do). > > Peace, > > Matt. > > From: basile pinsard <[email protected]> > Date: Monday, March 17, 2014 11:22 AM > To: Matt Glasser <[email protected]> > Cc: "Harms, Michael" <[email protected]>, Donna Dierker < > [email protected]>, "[email protected]" < > [email protected]> > > Subject: Re: [HCP-Users] subdivide parcellation > > ok I think I will adapt the MNE code to do the job as I am interested > into subdividing the existing parcellation rather than creating a random > one. > many thanks for your replies. > cheers > > basile > > > On Mon, Mar 17, 2014 at 4:12 PM, Glasser, Matthew <[email protected] > > wrote: > >> 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 <[email protected]> >> Date: Monday, March 17, 2014 10:04 AM >> To: basile pinsard <[email protected]>, Donna Dierker < >> [email protected]> >> >> Cc: "[email protected]" <[email protected]> >> 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: [email protected] >> >> From: basile pinsard <[email protected]> >> Date: Monday, March 17, 2014 9:51 AM >> To: Donna Dierker <[email protected]> >> Cc: "[email protected]" <[email protected]> >> 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 >> <[email protected]>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 <[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 >> >> >> ------------------------------ >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. 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If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > > > ------------------------------ > > 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
