Autobids has stopped working

#1

Hi colleagues,

I have set up an autobids for our project SEMINOWICZ^CLAUSTRUM back in Jan 2024 and it has been working well until Mar 2024. However, I cannot find the processed data collected after 7 Mar in the depository. We have been collecting new data in May and June. I should be grateful if anyone could help looking into the problem.

By the way, I have an account at the autobids portal (https://autobids-uwo.ca/index) but I cannot access my study. I have also submitted a query through the Google form https://docs.google.com/forms/d/15HSYFrIL6GnUvU4xmLAXwqcprtItDdhzloq8kxbu_Rs/viewform?ts=5c0194e8&edit_requested=true but hasn’t heard back yet. Which platform should I use to contact colleagues working with autobids?

Best regards,
Chun Yin

#2

Hi Chun Yin,
This is the correct forum to post questions - we are a bit backlogged since we haven’t had dedicated staff on this (should be rectified soon), but will do our best to help. I see your study on the system, and something seems to have gotten stuck early April. Will see if I can get it un-stuck, and restart things - but it looks like you have changed your patient numbering scheme part way? ie I see 9005, then 9005_2 – if you want these as two sessions, instead of the current flat structure (no session), may need to rename and re-run the conversion. Let me know what you prefer. I can grant you access to the study config UI so you can rename the files as well.

Ali

#3

Hi Ali,

Thank you so much for getting back. Actually we have run a second visit for our participants - that’s where the underscore 2 comes from. I think the participants from the second visit is not named consistently, so it is better for me to rename them by myself.

Some scans in visit 2 are the same as visit 1. Will it cause a problem in the conversion? In that case, it is better to use a hierarchical directory structure with different sessions.

I have submitted a autobids request earlier through both the website and the google form. I will provide more details in a separate email if there is manpower to work on it (or just post them here, if you prefer).

Thanks again for your help!

Best regards,
Chun Yin

#4

Hi Chun Yin,

I’ve granted you access to the study now, you should be able to log in now, and rename the tar files. If you want to keep the same flat hierarchy, you can include the visit in the subject identifier (e.g. 9001v1, 9001v2). To use the session field you would have to update “Tar2bids Patient Name Search String” in the Study Config, from *_{subject} to e.g. *_{subject}v{session}.

Let me know if you run into any issues.

#5

Hi Ali,

Thanks for helping with the access. I will explore with the system!

Best regards,
Chun Yin

#6

[Sorry for the duplicate email as Discourse was down last week]

Hi Ali,

I am writing to seek help for rerunning the autobids and starting a new project. My project is a longitudinal study with 5 visits per participant, and I have been collecting data for the second visit. We think that it is better to organize our scans in a hierarchical structure (I think it is different visits under the same subject, rather than the other way round?). The scans have been renamed, and some scans across visits will be partially overlapping (e.g., both visit 1 and 3 will have a resting state scan, but the tasks are different). I am thinking of reconfiguring the first visit and starting a new autobids session for the second visit. There is a DTI scan in the second visit, and I wonder if it is possible to add prepdwi to the pipeline.

I understand that there may not be enough manpower to help currently. I would be really grateful if you could help with the study configuration, but I am also happy to learn how to do the configuration myself if that is possible. Please let me know what works best for our case so we can discuss the next step.

Best regards,
Chun Yin