[RESOLVED] Error in 'hcp_asl'

Use Questions
1

Hi,

I am trying to use Qunex to process a HCP-D sample (HCD0122317_V1_MR).

Qunex docker version is 1.3.0. Gradcoeff file I used is the example from HCP github.

The mapping and parameters files are attached (similar to the ones in ‘quick start’).

HCPD001_mapping.txt (124 Bytes)

HCPD001_parameters.txt (4.3 KB)

I have successfully done hcp_pre_freesurfer, hcp_freesurfer, and hcp_post_freesurfer, then I tried to process asl data:

qunex_container hcp_asl
–sessionsfolder=“${STUDY_FOLDER}/sessions”
–batchfile=“${STUDY_FOLDER}/processing/batch.txt”
–container=“${QUNEX_CONTAINER}”
–hcp_gdcoeffs=“${GRADCOEFF}”

The errors were like this:

Running HCP ASL Pipeline [HCPStyleData] … —> Gradient distortion coefficients file present. ERROR: ‘task’ ERROR: Unknown error occured: … Traceback (most recent call last): File “/opt/qunex/python/qx_utilities/hcp/process_hcp.py”, line 11248, in hcp_asl if v[“name”] in [“PCASLhr”] or “SpinEchoFieldMap” in v[“task”]: ~^^^^^^^^ KeyError: ‘task’ …

Could you please kindly help me solve this? Thanks a lot.

Best,

Wilson

2

Hi Wilson,

Can you upload your session_hcp.txt file for this session or for one session (${STUDY_FOLDER}/sessions/<SESSION_ID>/session_hcp.txt). Based on the error and based on the mappng file, I am quite sure that ASL data was not mapped correclty.

Best, Jure

3

Hi Jure,

Please see my session_hcp.txt file for this session.

session_hcp.txt (4.5 KB)

Could you please advise me on how to map ASL data correctly? Thank you very much.

Best,

Wilson

4

Of course, can you also please upload your current mapping file so I can amend it. Thanks!

Best, Jure

5

Can you try with the attached session_hcp.txt. Yours had a weird empty column at the beginning.

session_hcp.txt (3.9 KB)

Also, I think ASL preprocessed data can be downloaded from HCP data bases? If that is an option for you, it could save you some time and resources.

Best, Jure

6

Thanks, Jure. The mapping file I used is the one I attached at the beginning. I tried the session_hcp.txt file you provided but the same errors occurred. HCP data bases currently don’t have processed ASL data, they will provide that in the next release.

Best,

Wilson

7

Hi,

I found a bug on our end, sorry for this. One of our latest updates broke something in ASL processing. There are a couple of ways here.

  1. You can use an older container. I think HCP folks used 0.99.2d for ASL processing. It is available via our docker hub.
  2. You can try using the patch I just coded. Download the file that is attached below. If you were to download it into /qunex/process_hcp.py then you force the container to use this file instead of the one inside with this parameter: --bind=/qunex/process_hcp.py:/opt/qunex/python/qx_utilities/hcp/process_hcp.py
  3. Wait for 1.3.2, there is no eta here, but I can fasttrack this patch if this is pressing for you (can get it out early next week probably).

Best, Jure

process_hcp.py (626.9 KB)

8

Thanks very much for the solutions, I will try them. Looking forward to the new version.

Best,

Wentao

9

Hi,

Any updates on this? We plan to test and release a new version of QuNex later this week or early next week.

Best, Jure

10

Hi Jure,

Thanks for the following-up. I am about to try again using version 1.4.1 singularity container on cluster. However, command “wget --show-progress -O qunex_suite-1.4.1.sif ‘https://jd.mblab.si/qunex/qunex_suite-1.4.1.sif’” didn’t work, seemingly due to trying to download a large file. After reading a old question here, I tried to git clone repo, but I could’t find the correct repo. Could you please advise me on how to get ‘qunex_suite-1.4.1.sif’? Thank you very much.

Best,

Wilson

11

Hi Wilson,

QuNex containers are quite large, so we only keep the last minor version uploaded in our cloud. The current one is 1.4.2, try

wget --show-progress -O qunex_suite-1.4.2.sif "https://jd.mblab.si/qunex/qunex_suite-1.4.2.sif"

It is “the same” as 1.4.1 with some minor bugfixes on top. We are in the process of releasing 1.4.3, which will be out sometime next week if all tests pass successfully.

Best, Jure

12

Hi Jure,

Thank you very much! I have successfully downloaded the 1.4.2 version.

Best,

Wilson