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 

Perfect, thanks!

 

czw., 3 paź 2019 o 00:49 Glasser, Matthew <[log in to unmask]> napisał(a):

 

 

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:

 

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]> 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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