[RESOLVED] Using import_HCP

Use Questions
#1

Hello, when attempting to use import_HCP we get a message that Qunex isn’t able to “parse” any of the files contained in the subject’s folders (see example output below), despite correctly identifying the files and where they are stored. Any idea why this might be the case? Here’s our command:

/cm/shared/qunex_container import_hcp --sessionsfolder=“/data/qnilab/AD_NPS_R01_2022_Test/HCP_YA/qunex/data/HCPYA_practice_100408/sessions” --inbox=“/data/qnilab/AD_NPS_R01_2022_Test/HCP_YA/qunex/data/100408” --archive=move --overwrite=yes --container=“/data/singularity-images/qunex_suite-0.95.3a.sif” --bind=“/data:/data”

Output:
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ERROR: Could not parse file: /data/qnilab/AD_NPS_R01_2022_Test/HCP_YA/qunex/data/100408/hcp/100408/MNINonLinear/Native/100408.L.sphere.reg.native.surf.gii

ERROR: Could not parse file: /data/qnilab/AD_NPS_R01_2022_Test/HCP_YA/qunex/data/100408/hcp/100408/MNINonLinear/Native/100408.thickness.native.dscalar.nii

ERROR: Could not parse file: /data/qnilab/AD_NPS_R01_2022_Test/HCP_YA/qunex/data/100408/hcp/100408/MNINonLinear/Native/100408.R.midthickness.native.surf.gii

ERROR: Could not parse file: /data/qnilab/AD_NPS_R01_2022_Test/HCP_YA/qunex/data/100408/hcp/100408/MNINonLinear/Native/100408.L.BA.native.label.gii

ERROR: Could not parse file: /data/qnilab/AD_NPS_R01_2022_Test/HCP_YA/qunex/data/100408/hcp/100408/MNINonLinear/Native/100408.L.ArealDistortion_FS.native.shape.gii
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#2

Hi,

It looks like you are trying to onboard pre-processed HCP data, we do not support this yet. We are intensively working on this and the May 2023 release will probably have this functionality in it. Right now you can only onboard unprocessed HCP-style data.

Onboarding processed HCP data takes a bit more effort as you need to do it manually and prepare some additional files yourself.

Kind regards, Jure

#3

Thanks. So if I just wanted to use Qunex to run hcp_icafix on HCP data that’s already been minimally preprocessed, could I just manually import this data into a subjID/hcp/subjID directory and have it work? Seems I would also need a batch.txt file in a /processing folder. How would I generate this batch.txt file?

#4

I will mark this resolved and continue the discussion in How to create Parameter, Batch and Mapping Files for HCP data that was preprocessed outside of Qunex.

We will prepare the guidance for this shortly.

Jure