I don't have a code snippet for you, but there is a separate "brain model" for each subcortical structure, which contains voxel indices. The "index map" that contains that brain model has the volume space information to turn them into coordinates in mm.
Note that for the cortex, the CIFTI files don't encode every vertex that exists in the gifti surface file. This is what the code Demian provided is doing, figuring out which vertices are represented in the cifti file. This is also different than how the fieldtrip matlab code does things. Tim On Tue, Aug 1, 2017 at 1:25 PM, Anand A Joshi <ajo...@usc.edu> wrote: > Thanks Matt for the reply. > > I figured out how to get it in Matlab (see below), but not in Python. I > can read cifti image in python. > > f=image.load_img(filename) > > But how do I get coordinates of the subcortical structures. I code snippet > would be appreciated. > > Thank you, > Best, > Anand > > ________________________________________ > From: Glasser, Matthew <glass...@wustl.edu> > Sent: Tuesday, August 1, 2017 11:07:53 AM > To: Anand Joshi; hcp-users@humanconnectome.org > Subject: Re: [HCP-Users] Reading Human Connectome Project (HCP) > *.dtseries.* file in Python > > For the volume structures these are in the CIFTI header, however for the > surfaces there are no veridical xyz coordinates, it all depends on the > surface model you are using. In general we recommend only using 3D > coordinates of individual subject¹s midthickness surfaces (or in special > circumstances white or pial surface. > > Peace, > > Matt. > > On 7/31/17, 9:07 PM, "hcp-users-boun...@humanconnectome.org on behalf of > Anand Joshi" <hcp-users-boun...@humanconnectome.org on behalf of > ajo...@ee.usc.edu> wrote: > > >I am trying to read .dtseries. grayordinate files from the human > >connectome project. I am using nilearn.image which is based on > >nibabel. > > > >f=image.load_img(filename) > > > >Now I want .pos filed from this file. I can get it in Matlab using: > > > >v=ft_cifti_read(filename) v.pos > > > >But nibabel does not create this field. How do I access it? > > > >Specifically, I want xyz coordinates of each of the grayordinates, How > >do I get those in python? > > > >Thanks, > >Anand > >_______________________________________________ > >HCP-Users mailing list > >HCP-Users@humanconnectome.org > >https://urldefense.proofpoint.com/v2/url?u=http- > 3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwIFAw&c= > clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=NnawZtcp5Dc- > cUxKIrTjKclBU0ay65KOACBdeM_HeW8&m=MlW84e0R9HVTEuuqVRxLJFr3bpV8Vw > _w61iEFP1hyjU&s=OnOaVBPwuVkIqJcjm_5ZXzm-m5P80IJ1jonjhayfqAs&e= > > > _______________________________________________ > 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
