So, the other list threads were about putting the MMP v1.0 into the volume as an MNI-space parcellation - the problem there is that the cortical alignment required for generating the MMP v1.0 is much tighter than current MNI alignment allows (and uses different features than most current volume registration methods), such that the volume-based cortical alignment is not good enough to keep the identity of the parcels separated, since the parcels are relatively small.
For a coarser parcellation in MNI space, it is possible to get it onto a surface representation, but it is somewhat tricky. In particular, you should avoid using a group average surface to do the mapping, because group average surfaces are missing large amounts of folding detail, and therefore won't align well with any cortical volume (not even an MNI template). This problem is unique to group average surfaces (and is more pronounced in areal feature aligned data, as aligning areal features reduces the alignment of folding, since they aren't particularly well correlated). A possibility for mapping such a volume parcellation to surfaces is to use many subjects, and map it to their MNI space atlas mesh surfaces, and then recombine it across subjects by finding, for each vertex, which label is most frequently used. Tim On Sat, Aug 27, 2016 at 6:06 PM, Harms, Michael <[email protected]> wrote: > Hi, > Do you mean project the volume-based parcellation onto HCP’s cifti surface > representation? That is somewhat of an artificial and ill-defined > operation, subject to various problems, as has been detailed by recent > threads involving Matt Glasser and Tim Coalson on this user list. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [email protected] > > From: Emily Kittelson <[email protected]> > Date: Saturday, August 27, 2016 at 8:59 AM > To: "Harms, Michael" <[email protected]> > Cc: "[email protected]" <[email protected]> > Subject: Re: [HCP-Users] HCP data and using a different atlas > > Thank you for the reply Mike Harms. To follow up, I am trying to convert > the Shen parcellation into a cifti surface+subcortical parcellation. Any > recommendations? > > I do plan on playing with the latest Glasser parcelation as well. > > Thank you, > Emily > > On Fri, Aug 26, 2016 at 3:42 PM, Harms, Michael <[email protected]> wrote: > >> >> IIRC, the Shen atlas is a volumetric parcellation, and probably in MNI152 >> space. The volume data in the MNINonLinear folders from the HCP Pipelines >> are also in MNI152 space, so in principle, should already be aligned with >> the Shen parcellation. >> >> We would encourage you to consider using a surface-based parcellation, >> such as the recent one from Glasser et al. >> https://balsa.wustl.edu/study/show/RVVG >> >> cheers, >> -MH >> >> -- >> Michael Harms, Ph.D. >> ----------------------------------------------------------- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave. Tel: 314-747-6173 >> St. Louis, MO 63110 Email: [email protected] >> >> From: <[email protected]> on behalf of Emily >> Kittelson <[email protected]> >> Date: Friday, August 26, 2016 at 3:33 PM >> To: "[email protected]" <[email protected]> >> Subject: [HCP-Users] HCP data and using a different atlas >> >> Hello, >> >> I am new to data processing and working on a grad project with HCP data. >> I have an atlas from Shen et at., 2013 (https://www.nitrc.org/frs/?gr >> oup_id=51) that I would like to apply to HCP data. What is the process >> for applying a different atlas to HCP data? >> >> Thank you in advance, >> Emily >> >> -- >> Emily Kittelson >> Center for Magnetic Resonance Research >> University of Minnesota >> 2021 6th St SE | Minneapolis, MN 55455 | Tel: 612-626-2001 >> >> _______________________________________________ >> 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. >> > > > > -- > Emily Kittelson > Center for Magnetic Resonance Research > University of Minnesota > 2021 6th St SE | Minneapolis, MN 55455 | Tel: 612-626-2001 > > > ------------------------------ > > 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
