Re: [HCP-Users] HCP data and using a different atlas

[Harms, Michael]

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: mha...@wustl.edu From: Emily Kittelson <colo0...@umn.edu> Date: Saturday, August 27, 2016 at 8:59 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 <mha...@wustl.edu> 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: mha...@wustl.edu From: <hcp-users-bounces@humanconnectome.org> on behalf of Emily Kittelson <colo0...@umn.edu> Date: Friday, August 26, 2016 at 3:33 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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/?group_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 HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users