cifti-separate

[Kenley, Jeanette]

Good evening,

I am trying to get only the cortex portions out of a dconn I have using cifti-separate.

I see the following error when I attempt to do so:

 wb_command -cifti-separate task-rest_DCANBOLDProc_v4.0.0_Atlas_smooth2.55.dconn.nii COLUMN -label CORTEX_LEFT cortexL.dconn.nii

While running:

/usr/local/pkg/workbench1.4.2/bin_linux64/../exe_linux64/wb_command -cifti-separate task-rest_DCANBOLDProc_v4.0.0_Atlas_smooth2.55.dconn.nii COLUMN -label CORTEX_LEFT cortexL.dconn.nii

ERROR: label separate requested on non-label cifti

When I load the dconn into matlab the structure label includes CORTEX_LEFT, CORTEX_RIGHT, etc, so I don't understand the error.

What am I missing please?

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[Glasser, Matt]

Perhaps it would be a good idea to take a step back and learn what your overall goals are here with the below command.

 

Also, in general we recommend using the official HCP Pipelines (https://github.com/Washington-University/HCPpipelines) or the Qu|Nex BIDS compatible containerized version of the HCP Pipelines (https://qunex.yale.edu/).  Other versions of the HCP Pipelines have not contributed their changes upstream and may not have the latest features and bug fixes from the official HCP Pipelines.  While forking the HCP Pipelines is technically allowed by the license (and may even contribute to the promotional efforts of others), it may not be good practice to use such pipelines for the aforementioned reasons and it is difficult to support such things or for us to know exactly what you are getting.  In general, unless there are major, unreconcilable disagreements in development, it is best for improvements to be contributed as patches to the main project so that everyone may benefit from them, rather than creating forks (especially without attempts to reconcile any differences at all).  Along these lines, the Qu|Nex project contributed many helpful patches and improvements to the HCP Pipelines and keep their container in sync with HCP Pipeline releases.  As a result, Qu|Nex is the official BIDS compatible containerized version of the HCP Pipelines.

 

Matt.

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

"label" in these commands refers to files where the data is named regions (dlabel), which is not appropriate for dconn.  -metric would work (but the output file should be named ending in .func.gii, as it doesn't output cifti), but I'm not sure why you want to create an additional large file with information that is already in the dconn.  We typically don't even make dconn files, as we can correlate on the fly instead.

If the file is correlations, you can instead restrict the dtseries to cortex, and then correlate that instead of generating the full dconn, but depending on what you intend to do next, there may be a way to avoid making any dconn files at all.  Another option is -cifti-restrict-dense-map, which would be fewer steps if you intend to restrict both dimensions of the dconn (most commands operate on one dimension at a time).

Tim

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From: Kenley, Jeanette <jkke...@wustl.edu>
Sent: Monday, October 18, 2021 10:28 PM

To: hcp-users <hcp-...@humanconnectome.org>
Subject: [hcp-users] cifti-separate

 

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[Kenley, Jeanette]

Sorry for the late reply as this email slipped through the cracks.

But thank you!

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From: Coalson, Timothy Scott (S&T-Student) <tsc...@mst.edu>
Sent: Tuesday, October 19, 2021 1:08 AM
To: hcp-users <hcp-...@humanconnectome.org>
Subject: [hcp-users] Re: cifti-separate

 

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