Compute volume (mm^3) subcortical regions

[Chris Racey]

Dear HCP experts,

I'm looking to calculate the volume (mm^3) for the 19 subcortical regions available within the Atlas_ROIs.2.nii.gz file.

I have used this for parcellating things like resting state data but I dont know how to go the extra step and find the volume for each of our subjects.

I have created a dlabel file for these regions in the following way.

wb_command -cifti-create-label subcortical_label.dlabel.nii -volume Glasser_et_al_2016_HCP_MMP1.0_qN_RVVG/MMP_dlabel/Atlas_ROIs.2.nii.gz Glasser_et_al_2016_HCP_MMP1.0_qN_RVVG/MMP_dlabel/Atlas_ROIs.2.nii.gz

For calculating things like surface area of cortical parcels we parcellate the computed MSMAll midthickness file. Is there anything equivalent for volumetric data?

Is there a way I can compute the volume of each subcortical region for my subjects?

Best wishes,
Chris

[Glasser, Matt]

Something like fslstats ${StudyFolder}/${Subject}/T1w/wmparc.nii.gz -l <key value> -u <key value> -V and take the second number in mm^3 should work.  An alternative would be fslstats -K ${StudyFolder}/${Subject}/T1w/wmparc.nii.gz ${StudyFolder}/${Subject}/T1w/wmparc.nii.gz -V.  You can look up the key values from this file: https://github.com/Washington-University/HCPpipelines/blob/master/global/config/FreeSurferAllLut.txt.

 

Matt.

--
You received this message because you are subscribed to the Google Groups "HCP-Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hcp-users+...@humanconnectome.org.
To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/8aea6944-ca35-4ca3-b313-131345b26104n%40humanconnectome.org.

 

---

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

[Harms, Michael]



${StudyFolder}/${Subject}/T1w/${Subject} contains all the usual direct output from FS itself.

 

So, if you simply want the subcortical volumes as computed directly by FS, you can look in ${StudyFolder}/${Subject}/T1w/${Subject}/stats/aseg.stats.

 

Cheers,

-MH

 

-- 

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, Matt" <glas...@wustl.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, May 11, 2022 at 8:25 AM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] Compute volume (mm^3) subcortical regions

 

* External Email - Caution *

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/C2D798DE-1D9C-4172-9AC0-FCDDAA9C78EA%40wustl.edu.

[Chris Racey]

Hi Matt and Michael,

Many thanks for this, it works great. 

For the benefit of future readers of this thread, here are the 19 labels and indices in the LUT...
labels={'CEREBELLUM_LEFT', 'THALAMUS_LEFT', 'CAUDATE_LEFT', 'PUTAMEN_LEFT', 'PALLIDUM_LEFT', 'BRAIN_STEM', 'HIPPOCAMPUS_LEFT', 'AMYGDALA_LEFT', 'ACCUMBENS_LEFT', 'DIENCEPHALON_VENTRAL_LEFT', 'CEREBELLUM_RIGHT', 'THALAMUS_RIGHT', 'CAUDATE_RIGHT', 'PUTAMEN_RIGHT', 'PALLIDUM_RIGHT','HIPPOCAMPUS_RIGHT', 'AMYGDALA_RIGHT', 'ACCUMBENS_RIGHT', 'DIENCEPHALON_VENTRAL_RIGHT'}';
%region indices (key values) for the 19 subcortical regions from the freesurferalllut.txt
keys={6:8,9:10,11,12,13,16,17,18,26,28,45:47,48:49,50,51,52,53,54,58,60}';

The values inside wmparc are integers so the thresholding needs take this into account, e.g. for the cerebellum_left

fslstats ${StudyFolder}/${Subject}/T1w/wmparc.nii.gz -l 5.9 -u 8.1 -V

Best wishes,

Chris

[Harms, Michael]



Personally, I would use the values that FS generates natively as part of stats/aseg.stats, which includes some sort of partial volume adjustment (rather than running fslstats on T1w/wmparc.nii.gz, which will not include the partial volume adjustment).  Obviously, the values should be similar however, and highly correlated.

 

-- 

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