Hi, Thanks for the hint, I will look at that example script from fMRI. As for the upsampling, I do it because some studies have shown that by upsampling directly the dwi you get better parametric maps. I was already upsampling to 1mm so I might as well register to structural space at the same time and get already registered parametric maps. Cheers,Jf
Sent from my Galaxy Tab® A<div> </div><div> </div><div>-------- Message d'origine --------</div><div>De : "Harms, Michael" <[email protected]> </div><div>Date : 2016/07/08 11:06 (GMT-05:00) </div><div>À : "Harms, Michael" <[email protected]>, Jean-Francois Cabana <[email protected]>, [email protected] </div><div>Objet : Re: [HCP-Users] Mapping volumetric maps on brain surfaces </div><div> </div> BTW: You should be able to do the sampling to the surface directly on DWI parameter maps processed at the native 2 mm acquisition resolution. No need to upsample the DWI to match the resolution of your structurals. -- 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]<mailto:[email protected]>> on behalf of "Harms, Michael" <[email protected]<mailto:[email protected]>> Date: Friday, July 8, 2016 at 10:01 AM To: Jean-Francois Cabana <[email protected]<mailto:[email protected]>>, " [email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Mapping volumetric maps on brain surfaces 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: [email protected]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of Jean-Francois Cabana <[email protected]<mailto:[email protected]>> Date: Friday, July 8, 2016 at 7:03 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[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. 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