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Homer3: Possible to preprocess many recordings at once?

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Posts: 7
Topic starter
(@inlava)
Active Member
Joined: 2 months ago

Hi experts,

With Homer3, I want to process 183 snirf files from 183 different study participants (every recording about 3 hours long).

I read in the forum that when I press RUN in the main GUI window and the processing level is set to group, it runs all the subjects ( https://openfnirs.org/community/homer3-forum/group-subject-run-levels-processing-stream/#post-872). However, my group output file in the derivatives folder is empty and in fact, only a couple of subjects seem to have run.

Is there any option to run all files loaded with on klick, or will I have to select each file to run the preprocessing?

Thank you very much in advance!

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Posts: 306
(@dboas)
Joined: 3 years ago

group run should work.

But wow, that is a lot of files. And long recordings for each file.

How long did it take to run all 183 files?

You saw the window pop up saying it was processing each of those files?

You should see the file highlight on the lower left propagate through the files as it advances.

I expect that this would take an hour or so or much longer given the current very slow snirf loader in Homer that uses the matlab HDF loader which seems to be horribly slow.

 

 

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Posts: 7
Topic starter
(@inlava)
Active Member
Joined: 2 months ago

Thanks for your fast reply.

Somehow, group run did not work for me, but I am very new to fNIRS and I am not sure whether I specified the .cfg file for a group run correctly, so that might be the problem. I only made my choices of processing steps for the subject level (at that is hmrR_Intensity2OD; hmrR_MotionCorrectWavelet, hmrR_MotionArtifact; hmrR_BandpassFilt; hmrR_OD2Conc).

When I run subject by subject, it takes 1.5 hours per subject. So I am now thinking about running the preprocessing on a more powerful machine...

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Posts: 7
Topic starter
(@inlava)
Active Member
Joined: 2 months ago

Also, I am running it on Matlab2017b, as at some point in the Wiki it was mentioned that it was best to use Matlab2017b.

I only learnt later, that this seems to be the case only for the runtime version of matlab ( https://github.com/BUNPC/Homer3/wiki/Download-and-Installation, first bullet point), but am now unsure about setting things up again on Matlab2023a.

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