Thanks for the response Demian. Matt.
On 8/1/17, 2:08 PM, "Demian Wassermann" <demian.wasserm...@inria.fr> wrote: >Hi Anand, > >as one of the guys who helped with the *first* implementation of CIFTI in >nibabel I can tell you that you need to navigate the header yourself. We >went for a first implementation which can effectively parse the header >and we are open for help in producing helper functions that will enable >people to easily do what you want. > >I don’t know how it is done in matlab but in python you’ll need the >accompanying surface. > >Assuming that you have it then, for the left cortex you can try: > >c = nibabel.load(cifti_filename) > >#this next line will fail if the required structure is not in the CIFTI >file. Also I’m assuming that the grayordinates are along the column >dimension >brain_model_cortex_left = [brain_model for brain_model in >c.header.get_index_map(1).brain_models if brain_model.brain_structure == >‘CIFTI_STRUCTURE_CORTEX_LEFT’][0] >vertex_indices = list(brain_model_cortex_left.vertex_indices) > >s = nibabel.load(gifti_left_surface_filename) >grayordinates_surface = s.darrays[0].data >grayordinates_cortex_left = [(brain_model_cortex_left.index_offset + i, >grayordinates_surface[v]) for i, v in enumerate(vertex_indices)] > > >Finally in grayordinates_cortex_left you’ll have a list of tuples where >the first element is the column in the CIFTI matrix and the second is >it’s grayordinate. > > > >Again, we just coded the bare bones to be able to implement the >convenience functionality on top of it, collaborations to the codebase >are more than welcomed. > >Best >Demian > >-- >Demian Wassermann, PhD >demian.wasserm...@inria.fr >Associate Research Professor (CR1) >Athena Project Team >INRIA Sophia Antipolis - Méditerranée >2004 route des lucioles - FR-06902 > > > > >> On 1 Aug 2017, at 20:39, Glasser, Matthew <glass...@wustl.edu> wrote: >> >> I would ask the author of the nilearn/nibabbel tools as I don’t know >> anything about the Python implementation of CIFTI. >> >> Peace, >> >> Matt. >> >> On 8/1/17, 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.humanconnecto >>>>me >>>> >>>>.org_mailman_listinfo_hcp-2Dusers&d=DwIFAw&c=clK7kQUTWtAVEOVIgvi0NU5BOU >>>>Hh >>>> >>>>pN0H8p7CSfnc_gI&r=NnawZtcp5Dc-cUxKIrTjKclBU0ay65KOACBdeM_HeW8&m=MlW84e0 >>>>R9 >>>> >>>>HVTEuuqVRxLJFr3bpV8Vw_w61iEFP1hyjU&s=OnOaVBPwuVkIqJcjm_5ZXzm-m5P80IJ1jo >>>>nj >>>> hayfqAs&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
