Hi , I’m trying to run HCP fMRIVolume/fMRISurface via Qunex recipe file for BIDS Data. I am able to sucessfully run till Post FreeSurfer, but the pipeline errors out at fMRI Volume. My BIDS func files exist, but the Left-Hand Side (LHS) shows nothing for BOLD and I get “NO BOLD images found” (screenshot attached).
Environment
QuNex: 1.3.1 docker image
HCP Pipelines via parameters.txt FreeSurfer via parameters.txt
OS: Linux (HPC)
Distortion correction: OFF
hcp_mapping_fmri.txt (54 Bytes)
batch.txt (1.9 KB)
Please find the attached batch and mapping files, also error and data images. Please let me know how can I proceed with this situation.
Dear Shashank,
Welcome to the QuNex forum.
A couple of questions so we can get to the bottom of this.
- In the mapping file, you also have a wm (working memory task I assume) BOLD mapping, but the batch file only has rest data. Is it OK for session 120 to only have rest data?
- It seems like you have multi echo data (rest echo-1, rest echo-2, rest echo-3 …). HCP Pipelines support processing of multi echo data, but you first need to manually prepare it. See [RESOLVED] QuNex, HCP-pipelines 4.8.0, and multi-echo fMRI - #4 by markushs for details. You need to merge this into a single image.
- If you execute number 2 and cleanup the data, you should have a single entry in the session file and then also in the batch file for rest. You can then map this entry as
bold rest => bold:rest. The left part of the mapping instruction needs to exactly match the image description. In your current state bold rest echo-1 => bold:rest would work, but this is wrong as it would only take echo-1.
Please, let me know if you need further assistance.
Best, Jure
Hi,
We plan to add auto merge functionality for multi echo BOLDs to QuNex’s import_bids command in the nearby future. Maybe as soon as into 1.4.1, which is to be released at the end of November if all goes to plan.
Best, Jure
Thanks for letting us know, we can shift to 1.41 once its’s done
This has been resolved, set --merge_multi_echo="yes" in the import_bids command and the session file will also include merged BOLDs that can be then mapped properly and used by HCP pipelines.
If something does not work, let me know. 1.4.1 should be released by the end of the week. Final tests are almost done.
Best, Jure
