How to map T1w/T2w contrast to the Desikan-Killiany atlas?
Melissa Thalhammer
(https://doi.org/10.1162/netn_a_00123). They recommend to use the “cifti-create-dense-from-template” and “cifti-parcellate” function, followed by “aparcstats2table” in Freesurfer.
Glasser, Matthew
I would:
- Process your structural data with the HCP pipelines (PreFreeSurfer, FreeSurfer, and PostFreeSurfer) so that you get T1w/T2w myelin maps properly mapped to the surface and in CIFTI files automatically.
- Use wb_command -cifti-parcellate with a parcellation that has structural and functional relevance, rather than simply using gyral and sulcal landmarks that do not have much relation to cortical areas. An example parcellation is available here: https://balsa.wustl.edu/file/show/3VLx.
- If you need the data outside of a CIFTI, you can convert to text with wb_command -cifti-convert -to-text <ParcellatedMyelin.pscalar.nii> <ParcellatedMyelin.csv> -col-delim “,”
It remains puzzling why folks keep using gyral and sulcal parcellations when multiple better options are available now.
Matt.
From: Melissa Thalhammer <melissa.tha...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Monday, July 26, 2021 at 9:10 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] How to map T1w/T2w contrast to the Desikan-Killiany atlas?
Dear experts,
I am trying to map T1w/T2w contrast myelin maps to the Desikan-Killiany atlas parcellation and have followed the publication by King et al., 2019 for this
(https://doi.org/10.1162/netn_a_00123). They recommend to use the “cifti-create-dense-from-template” and “cifti-parcellate” function, followed by “aparcstats2table” in Freesurfer.
I have T1T2.nii files and
tried to first convert them into cifti and then follow the description from above, but I got the warning
in the attached file. Moreover, aparcstats2table requires the --meas (measurement) flag which specifies the measure that should be extracted (select from area, volume, thickness, meancurv, foldind, curvind - but not myelin map which is unitless...). I have
tried to run it with the default --meas area flag, but Freesurfer automatically looks for the stats file, which is not available in the cifti-T1T2.nii file.
Does anyone have some tips?
Best,
Melissa Thalhammer
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Melissa Thalhammer
Coalson, Timothy Scott (S&T-Student)
Sent: Monday, July 26, 2021 11:46 AM
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Subject: Re: [hcp-users] How to map T1w/T2w contrast to the Desikan-Killiany atlas?