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Your ROI needs to be on the surface for you to be able to measure cortical thickness. How did you generate this ROI?
Once you have an ROI on the surface you can use these Connectome Workbench commands:
wb_command -metric-vertex-sum ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.thickness.32k_fs_LR.shape.gii -roi <${Hemisphere}_your_surface_roi.func.gii>
Gives you the sum of the cortical thickness across all vertices in the ROI
wb_command -metric-vertex-sum <${Hemisphere}_your_surface_roi.func.gii> -roi <${Hemisphere}_your_surface_roi.func.gii>
Gives you the number of vertices in your ROI
You can then divide the number from the first command by the number from the second command to give you the mean cortical thickness from your ROI. Not that this does not weight the mean thickness according to the surface area that each vertex contributes,
which might be the more correct thing to do. Let me know if you want us to tell you how to do that.
Peace,
Matt.
From: Jessica Jesser <[email protected]>
Date: Thursday, March 20, 2014 11:24 AM To: "[email protected]" <[email protected]> Subject: [HCP-Users] cortical thickness of a roi - freesurfer Dear HCP-Freesurfers,
I'd like to extract the mean cortical thickness of a ROI I generated for subjects from the human connectome project (HCP). The ROI is a mask in nifti format and its dimensions correspond to the HCP_subject/MNINonLinear/T1w_restore_brain.nii.gz file. I'd
like to use the normalized, structural HCP data from the preprocessed Freesurfer pipeline. Trying to follow the instruction on the Freesurfer Wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness),
I encountered several problems. I hope you can help me!
How do I map the subject thickness data to the fsaverage subject? There are several "thickness" files in the HCP dataset - which one should be used? I created a "surf" folder and filled it with the supposedly relevant files. Is the used file for the --surfreg
flag correct (see command line below)?
I tried to use the following command:
mri_surf2surf --srcsubject 100408 --srcsurfval 100408.R.thickness.32k_fs_LR.shape.gii --trgsubject fsaverage --trgsurfval rh.checkthickness.fsaverage.mgh --hemi rh --surfreg 100408.R.sphere.reg.native.surf.gii
This error message resulted:
Source registration surface changed to 100408.R.sphere.reg.native.surf.gii
Target registration surface changed to 100408.R.sphere.reg.native.surf.gii
srcsubject = 100408
srcval = 100408.R.thickness.32k_fs_LR.shape.gii
srctype =
trgsubject = fsaverage
trgval = rh.checkthickness.fsaverage.mgh
trgtype =
srcsurfreg = 100408.R.sphere.reg.native.surf.gii
trgsurfreg = 100408.R.sphere.reg.native.surf.gii
srchemi = rh
trghemi = rh
frame = 0
fwhm-in = 0
fwhm-out = 0
label-src = (null)
label-trg = (null)
OKToRevFaceOrder = 1
Reading source surface reg /usr/local/freesurfer/subjects/100408/surf/rh.100408.R.sphere.reg.native.surf.gii
Loading source data
** failed to open GIFTI XML file '/usr/local/freesurfer/subjects/100408/surf/100408.R.thickness.32k_fs_LR.shape.gii'
MRISreadGiftiAsMRI: gifti_read_image() returned NULL
ERROR: could not read 100408.R.thickness.32k_fs_LR.shape.gii as type 27
I appreciate your help.
Cheers,
Jessica
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- [HCP-Users] cortical thickness of a roi - freesurfer Jessica Jesser
- Re: [HCP-Users] cortical thickness of a roi - freesu... Glasser, Matthew
