On Sat, Jun 16, 2018 at 8:36 PM, Parvathaneni, Prasanna < [email protected]> wrote:
> Hi All, > > Thank you for suggesting “ciftify” on non-HCP datasets. We are trying to > run HCP pipeline using “ciftify" tool on our custom dataset and have few > questions > > - For running recon-all can we use Freesurfer v6. Suggested version > for HCP (Freesurfer 5.0.3_HCP) seem to have compatibility issues on Ubuntu > 16.08 as mentioned in below thread > > https://www.mail-archive.com/[email protected]/msg04158.html > The ciftify pipeline is not the HCP pipelines. It is a workaround for studies that don't follow HCP acquisition guidelines, to be able to get some (but not all) of the advantages of the HCP preprocessing methods. I would expect that it can accept freesurfer v6 output, but I don't know for sure. > > - Do you have any scripts for transforming diffusion data that is > aligned to subject T1 into “cifti” space similar to ciftify_subject_fmri > for FMRI data > > We haven't released tractography results for HCP data due to unsolved issues with tractography in general ("gyral bias"). You can run tractography using surface-based counting, and surface-based cortical results make sense to convert to standard grayordinate space. However, the diffusion/fiber direction information is most definitive in the white matter, while our standard grayordinate space only covers gray matter, so it would not make sense to convert that into grayordinate space. > Appreciate your feedback. > > Thanks > Prasanna > > > > > > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
