Offline QC of QSIprep outputs using dmriprep-viewer?

Software Support
1

hi there, general question about QC possibilities using dmriprep-viewer
i’m new to a lot of these tools, so bear with the basic question

i’m on a HPC server (running Rocky8) and am not sure if the web version of dmriprep-viewer is going to work there after i obtain QSIprep outputs. if we can’t figure it out or isn’t allowed (e.g. PHI restrictions) is it possible to install dmriprep-viewer and QC on a local laptop?

like, just follow these directions to install NodeJS and yarn?

thanks for your thoughts/recommendations

2

Hi @stbmtx,

You can only download the dwiqc.json files onto your local machine (only a few megabytes each) and run the dmriprep viewer webapp on your local machine.

Best,
Steven

1 Like
3

awesome, thanks! wasn’t sure what was minimally viable. a few MBs per subject is totally fine. i tested a copied-and-reduced version of the output directory and was able to get away with the following and still have dmriprep-viewer open nicely:

Screenshot 2024-11-08 at 10.27.10 AM

i did that online, though. i’ll work on the local dmriprep-viewer install later
thanks again @Steven

4

Hi @stbmtx,
No problem! Just as a minimal-storage example of what works for dmriprep viewer on my local machine, the folder I upload looks like this:

ROOTFOLDER_UPLOADED_TO_DMRIPREP_VIEWER
├── dwiqc.json
├── sub-1
│   └── ses-1
│       └── dwi
│           └── sub-1_ses-1_dwiqc.json
├── sub-2
│   └── ses-1
│       └── dwi
│           └── sub-2_ses-1_dwiqc.json
...

Best,
Steven

5

oh man, you’re right. further deletions into that structure also worked

6

Hi @stbmtx,

The application works purely client side when accessed on dmriprep-viewer, so I can’t see any reason to do any local install (but I might be missing something).

Cheers,
Ariel

7

hey there @Ariel_Rokem

yeah i was just trying to think ahead about trying to use it on our HPC server where the data will be, and which i’m kind of new to so have never even tried to opened a browser on.

but now that i know i can just download those minimal files to a local computer i’ll just do that and not bother with a local install of dmriprep-viewer. sorry to be unclear about my final decision and thanks!

-s

1 Like