Right. Matt. From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Emma Robinson <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Thursday, October 3, 2019 at 2:17 AM To: "[log in to unmask]" <[log in to unmask]> Subject: Re: [FSL] FW: [FSL] MSM - from fs_LR to native space Just to clarify the MSMSulc native sphere are these ones *Native/*.sphere.MSMSulc.native.surf.gii Right Tim/Matt? Thanks Emma On Thu, 3 Oct 2019 at 00:16, Jan Kurzawski <[log in to unmask]<mailto:[log in to unmask]>> wrote: Perfect, thanks! czw., 3 paź 2019 o 00:49 Glasser, Matthew <[log in to unmask]<mailto:[log in to unmask]>> napisał(a): From: Timothy Coalson <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: Timothy Coalson <[log in to unmask]<mailto:[log in to unmask]>> Date: Wednesday, October 2, 2019 at 5:45 PM To: "Glasser, Matthew" <[log in to unmask]<mailto:[log in to unmask]>> Subject: Re: FW: [FSL] MSM - from fs_LR to native space The HCP pipelines should generate 32k_fs_LR surfaces for your subject, which can display the MMP group parcellation as-is. Surface data is not inherently tied to coordinates, so you can display it on either the T1w-space or MNINonLinear-space surface files, with no additional commands. To resample the parcellation onto the subject's native mesh, use the fs_LR 32k atlas spheres and the MSMSulc registered native mesh spheres with either wb_command -cifti-resample, or -label-resample after using -cifti-separate. The atlas spheres are here: https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/standard_mesh_atlases wb_command doesn't care where files are located, it is only the pipeline scripts that require particular file naming and organization. Tim On Wed, Oct 2, 2019 at 5:32 PM Glasser, Matthew <[log in to unmask]<mailto:[log in to unmask]>> wrote: From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Jan Kurzawski <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Wednesday, October 2, 2019 at 8:54 AM To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> Subject: [FSL] MSM - from fs_LR to native space Dear FSL experts, I am using MSMSulc in the HCP pipeline to register subject’s native surfaces to the fs_LR template. After obtaining all the files i.e L.sphere.LR.reg.surf I would like to use them to map the cortical parcellation provided by Glasser et al. (*.dlabel.nii that is on the 32k_fs_LR surface) to the native space of my subject and later on project it on my freesurfer mesh I am a bit lost which msm command to use and where to put the MSM generated reg files. Kind regards, Jan ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ 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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