Creating mapping file for BIDS

Use Questions
1

Hello. I’m struggling with creating the mapping file. My data is in BIDS format. I ran the “import_bids” command successfully, however I’m not sure how to proceed. I’m attaching a photo of some of my data.

Thank you in advance,

Noga

image
image1214×406 63 KB

2

Hi Noga,

Welcome to the QuNex forums!

If import_bids was successful it should generate a file called session.txt in <study_folder>/sessions/<session_id>. That file is your starting point for mapping file preparation. If you upload it here or paste its contents here, I can help you out.

Best, Jure

3

Thank you for the response!

session.txt was not created, but I didn’t get an error message when running import_bids. How should I troubleshoot?

4

Please provide the following:

  • The full and exact call to import_bids, with all parameters.
  • The logs of the run (found in <study_folder>/processing/logs). There are probably 2 relevant logs there one in the runlogs subfolder and the other in the comlogs.

Best, Jure

5

OK I was able to fix the issue I had with import_bids and a session.txt file was created. here it is:

Generated by QuNex 1.3.0 [QIO] on 2025-12-03_10.11.22.582615

session: 1008
subject: 1008
bids: /home/docker/volumes/hcppipelines/NogaStudy/data/sessions/1008/bids
raw_data: /home/docker/volumes/hcppipelines/NogaStudy/data/sessions/1008/nii
hcp: /home/docker/volumes/hcppipelines/NogaStudy/data/sessions/1008/hcp

1: T1w ce-corrected :DwellTime(9.8e-06)
2: T1w ce-uncorrected :DwellTime(9.8e-06)
3: T2w ce-uncorrected :phenc(RL):DwellTime(2.6e-06):UnwarpDir(x)
4: FLAIR :phenc(RL):DwellTime(6e-06):UnwarpDir(x)
5: epi dir-PA acq-dwi :se(1) :EchoSpacing(0.000770008):phenc¶:DwellTime(2.6e-06):UnwarpDir(y)
6: epi dir-AP acq-func :se(2) :EchoSpacing(0.000570006):phenc(AP):DwellTime(2.5e-06):UnwarpDir(y-)
7: epi dir-PA acq-func :se(2) :EchoSpacing(0.000570006):phenc¶:DwellTime(2.5e-06):UnwarpDir(y)
8: bold emotionalnback :EchoSpacing(0.000575072):phenc(AP):DwellTime(2.5e-06):UnwarpDir(y-)
9: bold rest :EchoSpacing(0.000575072):phenc(AP):DwellTime(2.5e-06):UnwarpDir(y-)
10: dwi dir-AP :se(1) :EchoSpacing(0.000770008):phenc(AP):DwellTime(2.6e-06):UnwarpDir(y-)
11: dwi dir-PA :EchoSpacing(0.000770008):phenc¶:DwellTime(2.6e-06):UnwarpDir(y)

6

Try this mapping:

T1w ce-uncorrected  => T1w
T2w ce-uncorrected  => T2w
epi dir-PA acq-dwi  => SE-FM-PA : se(1)
epi dir-AP acq-func => SE-FM-AP : se(2)
epi dir-PA acq-func => SE-FM-PA : se(2)
bold emotionalnback => bold:task : se(2)
bold rest           => bold:rest : se(2)
dwi dir-AP          => DWI:dir_AP : se(1)
dwi dir-PA          => DWI:dir_PA : se(1)

This is used to inform QuNex about what exactly each image is and how to pair SE FMs with imaging data.

I have no data and wrote this from the top of my head, so maybe some adjustments will be needed. Once you run create_session_info. A file called session_hcp.txt will be created. You can upload its contents here so I can check if this worked. Also, for readability, you can mark the contents as code (triple back tick sign in this forum) so it is formatted as above.

Some more info about htis can be found at QuNex quick start using a container — QuNex documentation and HCP Pipeline Mapping in QuNex — QuNex documentation.

Note that if others sessions in the study have different acquisition protocol or image naming than this mapping won’t work for all of them. Good data has all sessions labeled the same way, so a single session file can be used across the whole session.

Best, Jure