[RESOLVED] Preprocess_conc for a subset of sessions

Use Questions
1

Hi

I was wondering if there is a way to run preprocess_conc command for a subset of sessions in the batch file without making a new batch file that contains those sessions-of-interest only.

Thanks
-Masih

2

Hi Masih!

Yes, you can filter (almost) every command so it runs only on a subset of sessions. A new filtering system was introduced in the latest version (0.94.4). You can provide the batch file via the --batchfile parameter. Next, you can use the --sessions or the --filter parameter to select a subset of sessions. With sessions you can only filter by session names, e.g.:

qunex preprocess_conc \
  --batchfile=/my_study/processing/batch.txt \
  --sessions="OP270_baseline,OP386_baseline"

The above command would run the preprocess_conc only over the two specified sessions. With the --filter parameter you have more flexibility when defining your subset. Inside the batch file each sessions has some additional information about it provided in the form of tag: value. Where tags are strings like session, subject, etc. With --filter you can select a subset of data based on values of these tags. Some tags are generated automatically by QuNex, and you can manually add additional tags into the batch file. For example, below we added the gender and group tags.

---
session: OP386_baseline
subject: OP386
dicom: /data/my_study/sessions/OP386_baseline/dicom
raw_data: /data/my_study/sessions/OP386_baseline/nii
hpc: /data/my_study/sessions/OP386_baseline/hpc

gender: male
group: control

Like mentioned, you can use the --filter parameter to select sessions based on tag values. For example by using:

qunex preprocess_conc \
  --batchfile=/my_study/processing/batch.txt \
  --filter="group:control|gender:male"

The command would be ran only on sessions that have the group tag value control and the gender tag value male. To filter over sessions use --filter=session:OP270_baseline,OP386_baseline. Note that older versions of QuNex used id tag instead of session, so check your batch file for what the exact tag should be when filtering.

Hope this answered your question. If you encounter any issues when running this, please let me know.