Using -cifti-separate will get you the 2mm definitions of these structures, in particular using "-volume-all <data> -label <structures>", but the same information is already available in the pipellines repository:
https://github.com/Washington-University/Pipelines/raw/master/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz There is also the 1.6mm definition: https://github.com/Washington-University/Pipelines/raw/master/global/templates/170494_Greyordinates/Atlas_ROIs.1.60.nii.gz However, if you want these at 0.7mm resolution, you would be better off generating them from the freesurfer outputs, because upsampling of binary classifications results in rough edges. Tim On Wed, Nov 22, 2017 at 9:00 AM, Xavier Guell Paradis <xavie...@mit.edu> wrote: > Dear Michael and Matt, > Thank you very much for your reply. > As for Michael's question - yes, I am looking for a dlabel file that > includes volumes such as caudate and putamen as separate structures. > Perhaps there is a workbench command that would allow to isolate these > structures in a random MNINonLinear dscalar file? > I have been exploring -cifti-restrict-dense-map and > -cifti-create-dense-scalar but have not figured it out. I have also tried > using python's nibabel and numpy tools to isolate the rows corresponding to > each structure, but this seems to be a much more complicated route. > > Thank you very much for your help, > Xavier. > > ------------------------------ > *From:* Harms, Michael [mha...@wustl.edu] > *Sent:* Tuesday, November 21, 2017 7:29 PM > *To:* Xavier Guell Paradis; hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] Subcortical atlas of > S900_AverageT1w_restore.nii.gz? > > > > Hi, > > > > The subcortical structures are already defined in the standard CIFTI > space. Are you just looking for a dlabel file that includes those > subcortical labels? > > > > 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 > <https://maps.google.com/?q=660+South+Euclid+Ave&entry=gmail&source=g>. > Tel: 314-747-6173 <(314)%20747-6173> > > St. Louis, MO 63110 Email: > mha...@wustl.edu > > > > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Xavier Guell > Paradis <xavie...@mit.edu> > *Date: *Tuesday, November 21, 2017 at 5:23 PM > *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *Subject: *[HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii. > gz? > > > > Dear HCP experts, > I was wondering if there is a publicly available, basic subcortical > parcellation (deliniating structures such as caudate and putamen) of the > standard volume structural file of HCP (such as S900_AverageT1w_restore.nii. > gz). > Restated, is there a parcellation that deliniates structures such as > caudate and putamen in S900_AverageT1w_restore.nii.gz? > Thank you very much, > Xavier. > > _______________________________________________ > 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. 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 > 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
