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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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