Merging subcortical and cortical dlabel.nii

[amirhussein.a]

Hi all,

I want to combine two .dlabel.nii files, one for cortical and the other for the subcorticals. I'm interested in using the resulting single dlabel file to convert the HCP's dense time-series into a parcel time-series using -cifti-parcellate. I couldn't find any straight-forward answer in the mailing list, thus posting this question. 

Best,

Amir

[Dierker, Donna]

Maybe cifti-separate to split the existing dlabel.nii into their components, then cifti-create to reassemble?

 

 

From: amirhussein.a <amirhu...@gmail.com>
Sent: Thursday, July 4, 2024 5:52 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] Merging subcortical and cortical dlabel.nii

 

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[J. A. Quent]

Hello Amir,

This sort of thing is very easy to do using the R package ciftiTools: https://github.com/mandymejia/ciftiTools

Here (https://github.com/mandymejia/ciftiTools/issues/61) is a similar use case where I used ciftiTools to create an ROI mask based on a differrent MNI .nii I had. You can do something very similar adding cortical and subcortical data into file.

You can find their paper here: https://www.sciencedirect.com/science/article/pii/S1053811922000076

Let me know if I can help.

Best,

Alex

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Fudan University, Shanghai China
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[Tim Coalson]

-cifti-create-dense-from-template is probably the best way to do this, to make sure the index order (and medial wall ROI, etc) matches another existing file.  You can specify the -cifti argument more than once, as long as there isn't more than one file containing a specific structure.  If your cortical parcellation is a 91282 grayordinates file (such that it represents subcortical indices, but sets them to the unlabeled key), then you first need to -cifti-separate the left and right hem data into .label.gii files, and then use those with the -metric repeatable option (instead of -cifti) in -cifti-create-dense-from-template.

https://www.humanconnectome.org/software/workbench-command/-cifti-create-dense-from-template

Tim

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[amirhussein.a]

Thank you all for the kind suggestions. I think using -cifti-create-dense-from-template was the way to go in my case. My cortical dlabel file was the MMP1 cortical (including ~60K) and the subcorticals had ~30K. I also had to add -label-collision SURFACES_FIRST flag for conflicting key values across two labels. For the input template to the command, I used MMP1_subcorticals dlabel file from here: https://balsa.wustl.edu/file/87B9N

Best,

Amir