Unfortunately the T2w images are pretty central to the HCP Pipelines and as a result not using a T2w image is not an officially supported analysis pathway (you cannot generate comparable surfaces and additional unreleased pipelines will depend on having the T1w/T2w myelin maps). Getting T1w-only data into the HCP Pipelines framework (i.e. CIFTI grayordinates) is possible to some extent, but requires a fair amount of hacking. The basic idea is to run FreeSurfer and your atlas registration outside of the HCP Pipelines, generating the appropriate files that match the names of the PreFreeSurfer and FreeSurfer pipeline outputs. You can use the PreFreeSurfer atlas registration module to do the atlas registration and perhaps some of the other PreFreeSurfer modules as they are useful to you. Then once you have FreeSurfer results and the files required for the first two modules of PostFreeSurfer, you can generate the grayordinates space and run some of the subsequent pipelines like the fMRI preprocessing pipelines and the diffusion pipeline. Currently unreleased pipelines for areal feature-based surface registration (which aligns cortical areal features instead of folding patterns for better cross-subject and cross-study alignment) and other subsequent pipelines will require T1w/T2w myelin maps. Thus, if you wish to take advantage of these things in future studies, you¹ll want to be acquiring T1w and T2w images going forward, together with field maps and your fMRI data. These will constitute the minimal acquisition requirements for the HCP Pipelines.
Note that the HCP list is a great venue for questions about how to acquire new neuroimaging data (i.e. before you start a new study) to take best advantages of HCP-style acquisition and analysis strategies, both currently released and things coming in the future. Peace, Matt. On 3/12/15, 3:13 PM, "Wang,Lihong" <[email protected]> wrote: >Dear HCP users/developers, > > >We did not collect T2 weighted images in our dataset. I am wondering >whether there is a pipeline script available for doing preprocessing >without T2 images? We do have fieldmap and MPRAGE images. Thanks for your >help. > > > >Best, > > >Lihong > >_______________________________________________ >HCP-Users mailing list >[email protected] >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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
