Of the cortex only or subcortical also? Matt.
From: Yael Shavit <yael.sh...@gmail.com<mailto:yael.sh...@gmail.com>> Date: Monday, January 28, 2019 at 1:55 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? I would like to compare diffusion properties of grey matter areas across subjects. I was wondering whether projecting them to individual native surfaces as they are would allowing comparing them to one another, or would it be better to project them all to MNI, and if so, how can I do so. Thanks again. בתאריך יום א׳, 27 בינו׳ 2019 ב-17:43 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: I guess you are going to have to be a lot more specific as to what kind of analysis you are trying to do. I guess that is the only way we will be able to give you good advice. Matt. From: Yael Shavit <yael.sh...@gmail.com<mailto:yael.sh...@gmail.com>> Date: Sunday, January 27, 2019 at 2:39 AM To: hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? Hi, thank you for your answers. My issue is not specifically with projection to surface, but with the fact that the diffusion data is in native space and not in common space (I am interested in working on cortical and subcortical the gray matter). Should I apply transformations to MNI and then project to the individual's surface in MNI for group comparison? Thanks again. בתאריך יום ו׳, 18 בינו׳ 2019 ב-0:32 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: If this is about tractography, the advice will be different however. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Thursday, January 17, 2019 at 12:57 PM To: Yael Shavit <yael.sh...@gmail.com<mailto:yael.sh...@gmail.com>> Cc: hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? The strongest directional information in the diffusion data is in the white matter, so I assume you are computing some measure from the scans and specifically want to study its value only in gray matter? The main command for this purpose is wb_command -volume-to-surface-mapping, and we recommend the ribbon mapping method (to capture the entire signal between white and pial surfaces, and downweight partial volumed voxels). We do not recommend downsampling the voxel data before this step, it would be better to use the 1.25mm^3 data directly. If you want the subcortical gray matter in our standard cifti space, then you should make a downsampled version for only that purpose (and still using the original 1.25mm^3 volume in the -volume-to-surface-mapping part). Note that you should generally do a small amount of smoothing (on the order of the larger voxel size) before downsampling volume files, in order to not effectively waste SNR, because the volume resampling methods are point estimates. You can look through the fMRISurface pipeline for how we go about doing this for fMRI data. Tim On Thu, Jan 17, 2019 at 10:42 AM Yael Shavit <yael.sh...@gmail.com<mailto:yael.sh...@gmail.com>> wrote: It seems that the diffusion HCP data is in native space in a resolution of 1.25mm^3. I am interested in projecting it to surface, in 2mm^3. What would be the best way to do so, preferably using the HCP Pipelines? Thank you in advance. Yael Shavit Tel Aviv University _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. 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