Re: [HCP-Users] volume to surface mapping

[Glasser, Matthew]

Hopefully you’ve already corrected your fMRI data for distortion in SPM?  If so, I would use FreeSurfer’s bbregister in a similar manner to how it is done in the fMRIVolume script: https://github.com/Washington-University/Pipelines/blob/master/fMRIVolume/scripts/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh line 401.  If you don’t care about getting subcortical data aligned across subjects, I suppose you could stop there. You can use an approach similar to what is in: https://github.com/Washington-University/Pipelines/blob/master/fMRISurface/scripts/RibbonVolumeToSurfaceMapping.sh lines 85-89 (and not use the goodvoxels.nii.gz file). Peace, Matt. From: Patrick Beukema <beuk....@gmail.com> Date: Monday, July 27, 2015 at 2:53 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] volume to surface mapping Thanks Matt- I could go down that route, but all of our preprocessing is done through SPM, and the actual functional data I am attempting to register is the result of many custom routines to generate specific searchlights, so ideally I was hoping for a way that would let me proceed with what I have. If I do proceed that way, is the t1w_restore the nifti to which functional data should be registered? Thanks, PB On Mon, Jul 27, 2015 at 3:29 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: Did you try running your raw functional data through the fMRIVolume and fMRISurface pipelines?  This is the recommended approach, and then you can analyze the data on the surface.   Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of Patrick Beukema <beuk....@gmail.com> Date: Monday, July 27, 2015 at 2:24 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] volume to surface mapping I am attempting to use the pipelines to look at functional data on the individual surface on my own (not HCP) data. I used the pre, free, and post hcp processing scripts and judging from the myelin maps, the output was good.  When I projected the functional activation to the surface (all in native space) using the wb_command -volume-to-surface-mapping, the functional activation was clearly very poorly aligned with the surface, to the extent that half of the brain activation map was missing. There are several t1_w nifti files that I could align the volume to and I am not sure which one to use. There is for example T1w_restore.nii, T1_restore.2.nii.gz, t1w.nii. Are there any guidelines on how to project functional data onto the surface in native space, or is this not the correct approach. Should the data be normalized to MNI and then projected to surface within MNI space. Thank you, _______________________________________________ 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.   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