The structures to specify to the -label option are CORTEX_LEFT and CORTEX_RIGHT (use the -label option twice).
Tim On Tue, Oct 30, 2018 at 6:35 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > Also use the label ones to make GIFTI label files. > > Matt. > > From: Leonardo Tozzi <lto...@stanford.edu> > Date: Tuesday, October 30, 2018 at 6:34 PM > To: Matt Glasser <glass...@wustl.edu> > Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and > subcortical parcellation > > Dear Matthew, > > > > Thank you for the very quick response. > > So for clarification, you would use the following command: > > > > wb_command -cifti-separate merged.dlabel.nii COLUMN -volume-all > subcort.nii.gz > > > > To obtain the subcortical volumes. > > What about the cortical ones? Is the file > Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii > already usable as input to FSL? I thought I would need a .gii file. Or do I > need to use the option in wb_command -cifti-separate: > > > > [-label] - repeatable - separate a surface model into a surface label file. > > In this case, what would be the argument for “<structure> - the structure to > output” ? > > Thank you very much, > > > > > > > > Leonardo Tozzi, MD, PhD > > Williams PanLab | Postdoctoral Fellow > > Stanford University | 401 Quarry Rd > <https://maps.google.com/?q=401+Quarry+Rd&entry=gmail&source=g> > > lto...@stanford.edu | (650) 5615738 > > > > > > *From: *"Glasser, Matthew" <glass...@wustl.edu> > *Date: *Tuesday, October 30, 2018 at 4:22 PM > *To: *Leonardo Tozzi <lto...@stanford.edu>, "hcp-users@humanconnectome.org" > <hcp-users@humanconnectome.org> > *Subject: *Re: [HCP-Users] Diffusion connectivity matrix with cortical > and subcortical parcellation > > > > I would separate the CIFTI file into GIFTI and NIFTI components with > wb_command -cifti-separate and follow the instructions for surface tracking > on FSL’s website. > > > > Matt. > > > > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Leonardo > Tozzi <lto...@stanford.edu> > *Date: *Tuesday, October 30, 2018 at 6:19 PM > *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *Subject: *[HCP-Users] Diffusion connectivity matrix with cortical and > subcortical parcellation > > > > To Whom it may concern, > > > > I have created a dlabel file by adding to the Glasser Parcellation from BALSA > the subcortical regions of the Freesurfer atlas. > > Now my goal would be to run a tractography analysis and obtain structural > connectivity matrices using this cortical+subcortical parcellation. Could > you suggest the simplest way to go from my dlabel file to something that is > compatible with diffusion software? I know that probtrackx accepts GIFTIs > as input, but I was wondering about how to extend this to subcortical > areas. Or rather would the simplest solution be to convert each subject’s > parcellation into a series of NIFTI files in native/standard space and > input these as ROIs into probtrackx? In this case, could you recommend the > correct series of workbench commands? I am also open to other software > recommendations besides the FSL suite. > > Thank you very much, > > > > > > > > Leonardo Tozzi, MD, PhD > > Williams PanLab | Postdoctoral Fellow > > Stanford University | 401 Quarry Rd > <https://maps.google.com/?q=401+Quarry+Rd&entry=gmail&source=g> > > lto...@stanford.edu | (650) 5615738 > > > > _______________________________________________ > 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. > > > ------------------------------ > > 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
