Thanks for your very helpful advice Tim, I am going to use ciftify.
Best, Frederic ________________________________ From: Timothy Coalson <tsc...@mst.edu> Sent: Tuesday, April 23, 2019 12:26:13 PM To: Briend, Frederic Cc: hcp-users@humanconnectome.org Subject: EXT MSG Re: [HCP-Users] Parcellation We recommend mapping the individual cortical data to surfaces before doing anything else with the data. If you have fieldmaps, and high-res T1w and T2w, you may be able to use the HCP pipelines to do this: https://github.com/Washington-University/HCPpipelines<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Washington-2DUniversity_HCPpipelines&d=DwMFaQ&c=o3PTkfaYAd6-No7SurnLt5qpge1aKYwPQyBFS7c8AA0&r=LGNx94TvRG6nkRaG0G6x1EEzuF6Nn2H9sSlvtmBZvIA&m=mfWENFs58zLxZjZlblR32R1bbCyUPMJGr9A-_f4oJ5g&s=BPQ_pqMqjN2vedxKgY0qkihzy5GPTm_WGMmnkFQ1wvk&e=> If you don't have these scans, another possibility is ciftify: https://github.com/edickie/ciftify<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_edickie_ciftify&d=DwMFaQ&c=o3PTkfaYAd6-No7SurnLt5qpge1aKYwPQyBFS7c8AA0&r=LGNx94TvRG6nkRaG0G6x1EEzuF6Nn2H9sSlvtmBZvIA&m=mfWENFs58zLxZjZlblR32R1bbCyUPMJGr9A-_f4oJ5g&s=uN3M2_gDx3n-uvW4ND5CWcoxzQ54wt4o3hOqSvwmF-c&e=> Either of these will output your data in cifti format, and you can then use wb_command -cifti-parcellate on it. You can accurately map the parcellation into an individual's volume space using their surfaces, but that uses the same information needed to map the subject's data to the surface anyway. However, it is generally not possible to accurately map the parcellation to group-averaged volume data, because existing volume registration does not achieve the same alignment precision across subjects that surface registration does, see our recent paper: https://www.ncbi.nlm.nih.gov/pubmed/29925602<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pubmed_29925602&d=DwMFaQ&c=o3PTkfaYAd6-No7SurnLt5qpge1aKYwPQyBFS7c8AA0&r=LGNx94TvRG6nkRaG0G6x1EEzuF6Nn2H9sSlvtmBZvIA&m=mfWENFs58zLxZjZlblR32R1bbCyUPMJGr9A-_f4oJ5g&s=9yVZu8VM7DfQFQqTmjWqwJ4jzxmj8CZbH4hDu2Lo1j4&e=> Tim On Tue, Apr 23, 2019 at 12:27 PM Briend, Frederic <fbri...@uabmc.edu<mailto:fbri...@uabmc.edu>> wrote: Dear hcp-users members, I would like to use a parcellation (Glasser's atlas 360), to reduce the dimensionality from my image (resting-state images in .nii) from voxels to parcels (averaging my timeseries across each parcel). How is it possible to do that, as advice by Matthew here<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FA2-3Dind1904-26L-3Dfsl-26F-3D-26S-3D-26P-3D244505&d=DwMFaQ&c=o3PTkfaYAd6-No7SurnLt5qpge1aKYwPQyBFS7c8AA0&r=LGNx94TvRG6nkRaG0G6x1EEzuF6Nn2H9sSlvtmBZvIA&m=mfWENFs58zLxZjZlblR32R1bbCyUPMJGr9A-_f4oJ5g&s=Xf5qAkLDf69gGk5LfEom8ikJ6x_rYZLMI1tXFxV4_l4&e=>, by the Connectome Workbench’s wb_command -cifti-parcellate ? Thanks a lot. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMFaQ&c=o3PTkfaYAd6-No7SurnLt5qpge1aKYwPQyBFS7c8AA0&r=LGNx94TvRG6nkRaG0G6x1EEzuF6Nn2H9sSlvtmBZvIA&m=mfWENFs58zLxZjZlblR32R1bbCyUPMJGr9A-_f4oJ5g&s=qU-Mcwx-6Q3yheHY7dyI108rKilha1pIiJT7kW6-_yQ&e=> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
