Commnad Line only Osprey

This is probably obvious, but reading through the Osprey doc (Osprey | osprey-documentation.utf8) I can’t figure out how to run osprey without the gui… like through the commands only


Alex W.

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There is a wrapper function in the osprey/utilities/ folder called RunOspreyJob.m that will do what you are asking.

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Thanks Mark!

Was this information somewhere? I couldn’t find it on the Osprey documentation site…


Alex W.

I don’t believe it is, no.

Hi Mark/Alex,

I just wanted to add that there are now some command line instructions in the Osprey documentation, located here.

Thanks for raising this,


Hi Chris (and others),

I have got Osprey running through the command line (Using RunOspreyJob(‘jobfile.json’)) . Works fine up until the MRSCont = OspreyOverview(MRSCont); step, most likely because I do not have a stat.csv file for the script to read and sort my data. How should this stat.csv file be organised? should it be like this?:


or should it be more like the job file?:
“group1”: [“/Path/To/sub-01_ses-01.sdat”,“/Path/To/sub-02_ses-01.sdat”,…,“/Path/To/sub-14_ses-01.sdat”]
“group2”: [“/Path/To/sub-01_ses-02.sdat”,“/Path/To/sub-02_ses-02.sdat”,…,“/Path/To/sub-14_ses-02.sdat”]

Also, in either setup, I assume I could use any naming structure for the group name - so for the first example I could just use:

Any help appreciated. I will post this as a standalone forum post as well.

Hi Paul,

My understanding is that OspreyOverview should skip all stat file-related code if one wasn’t provided. If you’re able to share the error, I’m happy to help with that.

Regarding the stat file organization, the simplest stat file simply has “group” as a heading, and a column of group indicators, with the order corresponding to the data files in your job file.

You can find an example included in the example data on Git (exampledata/sdat/MEGA/stat.csv).

Hope that helps,

Thanks Chris,

Helge helped me over on the other post. I created a stat.csv file, and re-ran the OspreyOverview step and it worked.
Note, (more for others who may read this) you really need at least two column titles, group and subject. I found that if I did not have a subject column, the code tried to make one, and for some reason it would give an error message. Including a column titled subject fixed that particular error.

Cheers, and Happy New Year!

Great! Glad to hear you got it working!

Happy new year!

Could you provide an example file for us? The one linked above did not have a Subject column

Hi @weberam2,

you can find an example here (Using stat.csv files with RunOspreyJob - #2 by Helge)