computing thickness/volume on HCP

[Sardaripour, Neda]

Dear HCP team,

I would like to calculate the thickness and/or volumes on the HCP dataset for customly defined cortical and subcortical brain regions.

Does the HCP workbench allow us to specify custom regions for computing volumes (e.g. as input masks)?

If not, could you recommend an alternative way to compute thickness/volumes? For example, one simple way would be by using the partial-volume outputs of FAST. Are these partial volume maps provided as part of the HCP dataset (I wasn't able to find them in the data).

 

I would really appreciate if you can give me some advice regarding this!

Many thanks,

Neda

 

[Glasser, Matthew]

You can compute the mean cortical thickness within a parcel using wb_command -cifti-parcellation.  For a subcortical ROI, it might be easiest to just us fslstats -V and use the second output. 

 

Matt.

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[Coalson, Timothy Scott (S&T-Student)]

You can also compute the per-vertex cortical volume map with the -surface-wedge-volume command.  It outputs a metric file, so you will need to compute for both hemispheres and then combine them into cifti format with -cifti-create-dense-from-template before you can use -cifti-parcellate.

Tim

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From: Glasser, Matthew <glas...@wustl.edu>
Sent: Tuesday, July 6, 2021 3:30 PM
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Subject: Re: [hcp-users] computing thickness/volume on HCP

 

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[Neda Sardaripour]

Thank you very much for your answers!

Just to clarify, the HCP does not provide partial volume estimates that can be used to compute subcortical gray matter volumes?

Best,

Neda

[Glasser, Matthew]

HCP data have much higher spatial resolution than typical datasets (0.7 or 0.8mm isotropic vs 1mm isotropic) and thus partial volume estimates are probably less important.  I don’t think FreeSurfer produces such estimates in any case.  For the cortical ribbon Connectome Workbench could produce such estimates if needed. 

Matt.

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[Harms, Michael]

 

IIRC, the subcortical volume estimates in the native “aseg.stats” file returned by FreeSurfer are adjusted for partial volume effects.

 

-- 

Michael Harms, Ph.D.

-----------------------------------------------------------

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.                        Tel: 314-747-6173

St. Louis, MO  63110                          Email: mha...@wustl.edu

 

From: "Glasser, Matthew" <glas...@wustl.edu>
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Date: Wednesday, July 7, 2021 at 4:37 PM
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Cc: "tsc...@mst.edu" <tsc...@mst.edu>
Subject: Re: [hcp-users] computing thickness/volume on HCP

 

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