My bad, basile. Matt told me the same thing Mike is saying below. Didn't mean to get your hopes up.
On Mar 17, 2014, at 10:08 AM, "Harms, Michael" <[email protected]> wrote: > > Just to clarify: The full pipeline output that Donna was referencing > includes "internal" pipeline outputs that we don't include in our released > "package" outputs. As of now, I don't believe there is any plan to > release the FS results in the native FS directory structure. > > 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] > > > > > On 3/17/14 9:58 AM, "Donna Dierker" <[email protected]> wrote: > >> Yes, we're working hard to release 500 subjects soon, and what I sent is >> based on the new pipeline. >> >> I guess this is a key difference. >> >> >> On Mar 17, 2014, at 9:51 AM, basile pinsard <[email protected]> >> wrote: >> >>> 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.pa >>> rcellation.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.00 >>> 60159 >>>> >>>> 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
