[RESOLVED] How to setup hcp_mapping.txt

Use Questions
1

Hello,

I’m experiencing difficulties importing BIDS data in a similar manner to what is described in this QuNex forum thread. I suspect I’m encountering a similar issue, but I’m not sure how to resolve it. I similarly run the following commands:

  1. create_study
  2. import_bids
  3. setup_hcp

The first two steps work without any issue. Here is the command I’m using for the third:

qunex_container setup_hcp \
  --sourcefolder="/test/sessions/003" \
  --sessions="003"  \
  --container="${QUNEX_CONTAINER}"

However, nothing seems to happen when I run it.

For additional context, my session.txt file looks like this:

# Generated by QuNex 0.100.0 [QX IO] on 2024-11-03_14.54.57.134370
#
session: 003
subject: 003
bids: /Users/user/qunex/test/sessions/003/bids
raw_data: /Users/user/qunex/test/sessions/003/nii
hcp: /Users/user/qunex/test/sessions/003/hcp

1: T1w  
2: T2w

The hcp folder doesn’t actually exist.
I’m unsure about how to configure the hcp_mapping.txt file. Could you help me on setting this up? I’d like then to run hcp_pre_freesurfer with --hcp_processing_mode=LegacyStyleData.

Thank you for your help

Davide

2

Hi Davide,

Is what you pasted the whole session.txt, meaning that you only have the two structural images? Or is is truncated?

An example of how to create and use the mapping file, can be found at QuNex quick start using a Docker container — QuNex documentation and HCP Pipeline Mapping in QuNex — QuNex documentation. When you have the mapping file, you run the create_session_info command which gives you a session_hcp.txt file that is then used by setup_hcp to properly prepare the hcp folder structure.

Best, Jure

3

Yes, I only have those two structural images.
Since my images are already called T1w and T2w the mapping should be trivial. I managed to run create_session_info , setup_hcp and create_batch.

I get the attached error when running:

qunex_container hcp_pre_freesurfer \
    --sessionsfolder="${STUDY_FOLDER}/sessions" \
    --batchfile="${STUDY_FOLDER}/processing/batch.txt" \
    --container="${QUNEX_CONTAINER}"

I attach also the used parameters.

error_hcp_pre_freesurfer_003_2024-11-05_17.41.24.494507.log (15.5 KB)
SD_parameters.txt (1.9 KB)

Thank you for your time and patience!

4

Hi,

At a glance it seems something is wrong with your imaging data, the first error says:

Error: file does not appear to be a valid NIFTI or ANALYZE image
Error: file does not appear to be a valid NIFTI or ANALYZE image

I imagine the error is repeated twice because it pops up once for T1w and then again for T2w.

Can you attach the ${STUDY_FOLDER}/processing/batch.txt so I have the full picture. Thanks!

Best, Jure

5

Thank you very much for your kind support! Everything now works just fine. The second error was related to hidden MacOs files that were interpreted as independent images. I solved the problem just by force delete them.

Best

6

Glad to hear that!

Best, Jure