If that is your interest, have you considered upsampling BEFORE preprocessing the DWI? That might be more likely to add information than upsampling after everything has been processed and aligned.
-Keith On Fri, Jul 8, 2016 at 10:10 AM, Jean-Francois Cabana <[email protected]> wrote: > 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 > > > -------- Message d'origine -------- > De : "Harms, Michael" <[email protected]> > Date : 2016/07/08 11:06 (GMT-05:00) > À : "Harms, Michael" <[email protected]>, Jean-Francois Cabana < > [email protected]>, [email protected] > Objet : Re: [HCP-Users] Mapping volumetric maps on brain surfaces > > > 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]> on behalf of "Harms, > Michael" <[email protected]> > Date: Friday, July 8, 2016 at 10:01 AM > To: Jean-Francois Cabana <[email protected]>, " > [email protected]" <[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] > > From: <[email protected]> on behalf of Jean-Francois > Cabana <[email protected]> > Date: Friday, July 8, 2016 at 7:03 AM > To: "[email protected]" <[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] > 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. 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