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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