fsl_onset_extraction Question

[hlmorgan8]

Hi there,

Apologies for another question but I am having trouble with the fsl_onset_extraction function in clpipe. I made a BIDS formatted events file (nback_events.tsv below) but I had some questions about the GLM Config File as well as the fsl_onset_extraction function.

1. When I try to run fsl_onset_extraction, I get an error saying "Error: no such option: -s" does this mean that submit should not be included? When I tried to run it without submit, nothing seemed to happen. Here is what I tried to run below: fsl_onset_extract -config_file /nas02/depts/hopfinger/hlmorgan/lumosity_output_2020/clpipe_config.json -glm_config_file /nas02/depts/hopfinger/hlmorgan/lumosity_output_2020/GLMConfigFile_1back.json -submit

2. Where should the event files be stored? I point the event file suffix to the correct document but I am confused about if it should be in the data_BIDS folder, fmri_prep folder, main folder etc.? Should it be in the target directory that I specified in the GLMSetupOptions portion of my config file?

3. For the TrialTypetoExtract, is how I did it below correct?

"Level1Onsets": { "EventFileSuffix": "nback_events.tsv", "TrialTypeVariable": "trial_type", "TrialTypeToExtract": [ "on", "off" ], "TimeConversionFactor": 1, "ParametricResponseVariable": "1", "EVDirectory": "/nas02/depts/hopfinger/hlmorgan/lumosity_output_2020/data_glm_1back/level1_1back/onsets_1back" },

Thank you in advance for any help!

-Hannah Morgan

[hlmorgan8]

Hey Teague! I just wanted to check in on this question, thank you in advance for any insight that you have!

[trh3]

My apologies for the delay! No, fsl_onset_extraction doesn't have a -submit argument, it doesn't require much computational power to run, so I don't submit it to any batch manager.

For your second question, are you asking about where the BIDS formatted event files go? Or the onset files that are generated by this command? The BIDS formatted event files go along side of the subject level scans. You should have 1 event file per scan per subject. The onset files that get generated go into any folder you'd like, but I like to put them into a data_onsets folder within the project directory.

Your TrialTypesToExtract should be the values in the trial_type column you would like to create onset files for. So if you have two trial types specified as "on" and "off," then that should work just fine.

[hlmorgan8]

Thank you, Teague. I am working on making one event file per participant per scan. However, when I was testing out fsl_onset_extract, I tried to use -debug and I didn't receive any errors (or any information at all). I know that I should be getting some errors because not everyone has an event file yet. Is that correct, should I not be getting any errors when I use -debug? Thank you in advance!