Dear Matt, Thank you for your answer. I read the paper, and things are much clearer now. I have another question though.
In addition to the parametric maps derived from DWI, we also have quantitative parametric maps (T1, T2*, PD and susceptibility) computed from a multi-parametric mapping sequence, acquired at the same resolution as our structural data (1mm isotropic). These maps will also be processed in the subject native space. As with the DWI maps, I would like to transfert them onto the subject surfaces, and perform group analysis. I would like to take advantage of the high-res 164k mesh since our maps have higher resolution than the 32k mesh (2mm). For what I understand, the 164k mesh exists only in the MNINonLinear space. My question is, should I transform the 164k_fs_LR mesh from the MNI space to the native space? Or do you think I still should use the 32k_fs_LR mesh in the native space? Or maybe I should rather transform our multi-parametric data in MNI space and use the 164k mesh? Many thanks, JF From: Glasser, Matthew Sent: Sunday, July 24, 2016 1:38 PM To: Jean-François Cabana ; [email protected] Subject: Re: [HCP-Users] Mapping volumetric maps on brain surfaces I would have a look at this paper: http://www.sciencedirect.com/science/article/pii/S1053811913005053 for a description of how the data are organized. If you want to compare the maps across subjects and the diffusion data are in the subject’s physical space, I would use the surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k Peace, Matt. From: Jean-François Cabana <[email protected]> Date: Sunday, July 24, 2016 at 7:03 AM To: Matt Glasser <[email protected]>, "[email protected]" <[email protected]> Subject: Re: [HCP-Users] Mapping volumetric maps on brain surfaces Dear Matt, I tried the –volume-to-surface-mapping as you suggested and it seems to work fine. However, I am a bit (a lot) confused by all the different spaces and surfaces, and I’m not sure which one to use. What I have are parametric maps computed in the native space of each subjects. What I want to do is map these parameters on the surfaces (and on subcortical GM structures), perform group averages and comparison. What surfaces should I map onto? I see surfaces files in : - T1w/Native - T1w/fsaverage_LR32k - MNINonLinear/Native - MNINonLinear/fsaverage_LR32k Thank you for your help, JF From: Glasser, Matthew Sent: Friday, July 8, 2016 7:00 PM To: Harms, Michael ; Jean-Francois Cabana ; [email protected] Subject: Re: [HCP-Users] Mapping volumetric maps on brain surfaces I wouldn’t do the up sampling. I also would use the -ribbon-constrained approach rather than the -myelin-style approach unless you want the maps weighted towards the midthickness. The command to use is wb_command -volume-to-surface-mapping. Peace, Matt. From: <[email protected]> on behalf of "Harms, Michael" <[email protected]> Date: Friday, July 8, 2016 at 10:06 AM To: "Harms, Michael" <[email protected]>, Jean-Francois Cabana <[email protected]>, " [email protected]" <[email protected]> Subject: 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. 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