Re: [HCP-Users] Mapping volumetric maps on brain surfaces

[Harms, Michael]

Hi, I’m not sure if such an example script exists.  You might have to wrestle with how the myelin maps are created a little bit — in particular, the parts related to -volume-to-surface-mapping and the resampling to a smaller mesh.  A very similar sort of thing happens in the fMRISurface pipeline as well (see RibbonVolumeToSurfaceMapping.sh). 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-boun...@humanconnectome.org> on behalf of Jean-Francois Cabana <jfcab...@outlook.com> Date: Friday, July 8, 2016 at 7:03 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Mapping volumetric maps on brain surfaces Dear HCP community,   I am using the HCP pipelines to process our data, which include a 1mm isotropic T1w, T2w and multiparametric, and a 2mm isotropic DWI sequences. I have modified the diffusion pipeline script so that the preprocessed DWI is upsampled to 1mm as it is registered to the native T1w (afterit’s been processed using the structural pipeline).   I am using the DWI to compute several parameters maps, from NODDI and DKI. What I want to do is map these parameters on the brain surfaces (pial, mid-thickness, inflated, ...), much like what is done with the myelin maps in the PostFreeSurfer pipeline. The goal is to compute individuals maps and also group average maps and compare between groups. I have no idea how to do that. I looked at the CreateMyelinMaps.sh script but it does not provides much comments/explanation, so I have no idea exactly what it is doing.   I will have several maps to transfer on the brain sufaces like this, as we will also compute quantitative T1, T2* and susceptibility maps in addition to NODDI and DKI maps. What I want is build a script that takes as argument a subject name (assuming file names and directories conventions from the structural preprocessing pipeline) and a path to a parametric volume map, that will perform the surface mapping and add the results to a the subject’s spec file. Surely I am not the first one to do that and a script like that must exists somewhere.   If anyone could provide me with an example script (with comments so I know what it is doing) that I could adapt, or direct me to a tutorial that explains how to do that, that would be of great help!   Many thanks in advance, JF       _______________________________________________ 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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users