wb_command -cifti-separate Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii COLUMN -label CORTEX_LEFT Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.label.gii
# resample template to 164k as the native output is 164k
wb_command -label-resample Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.label.gii L.sphere.32k_fs_LR.surf.gii 100307.L.sphere.164k_fs_LR.surf.gii BARYCENTRIC Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.164k_fs_LR.label.gii
# reg to native
wb_command -label-resample Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.164k_fs_LR.label.gii 100307.L.sphere.164k_fs_LR.surf.gii 100307.L.sphere.MSMSulc.native.surf.gii BARYCENTRIC left.native.label.gii
# move to FS (source needed avoid the osx Symbol not found)
source /Applications/freesurfer/SetUpFreeSurfer.sh;mris_convert --annot left.native.label.gii 100307.L.sphere.MSMSulc.native.surf.gii ./lh.HCP-MMP1.nat.annot
Best,
Jan
Just to clarify the MSMSulc native sphere are these ones*Native/*.sphere.MSMSulc.native.surf.gii
Right Tim/Matt?
Thanks
Emma
Perfect, thanks!
From: Timothy Coalson <[log in to unmask]>
Reply-To: Timothy Coalson <[log in to unmask]>
Date: Wednesday, October 2, 2019 at 5:45 PM
To: "Glasser, Matthew" <[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:
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]> wrote:
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Jan Kurzawski <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Wednesday, October 2, 2019 at 8:54 AM
To: "[log in to unmask]" <[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
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