BIDS/SPM does not recognize --config flag on participant level

Hi guys,

does anybody use BIDS/SPM App?

I use this command:

docker run -ti --rm
-v /tmp:/tmp
-v /var/tmp:/var/tmp
-v /path/to/local/bids/input/dataset/:/data
-v /path/to/local/output/:/output
/data /output participant --participant_label 01 --config pipeline_participant.m

In the template file I have only changed fwhm, and voxel sizes. (vox_anat = [1 1 1];vox_func = [3 3 3];FWHM = [12 12 12]; to (vox_anat = [1 1 1];vox_func = [2 2 2];FWHM = [4, 4, 4];))

template config file:

BIDS/SPM simply ignores the flag and uses default settings (vox_anat = [1 1 1];vox_func = [3 3 3];FWHM = [12 12 12]) without any errors.

I have tried simply to remove the file and to launch the same command again. Nothing changed, so I think it simply ignores the flag.

Does anybody has any ideas?

I would very apriciate any help!



Dear Dima,

I doubt the BIDS/SPM App is very much used at all, especially as it would require a lot more documentation.

I think what happens in your case is that the default configuration file is used because the one you specify has the same name than default and does not use a full path:

What you have to do is put the configuration file somewhere accessible from within the container, e.g. in /path/to/local/bids/input/dataset/code/pipeline_participant.m and pass it along in the command line using --config /data/code/pipeline_participant.m.

I am also going to update the BIDS App to use the latest version of SPM12 (r7487). It would be great if you could then try it out.

Best regards,

Thank you very much for your response!

Indeed, this solved the problem! Yes, I would be very glad to try it out! It is very a usefull package for people who use SPM for the entire data analysis.

Do you maybe have any template for a config file for the first level analysis? Should I run the first lavel analysis on participant or on group level of BIDS/SPM?

Thank you very much!

Best regards,


Great! The SPM BIDS App was updated yesterday to use SPM12 r7487 and MATLAB R2018b:

and you can refresh your local image with docker pull bids/spm.

An fMRI first level analysis would be running at the participant level in a BIDS App. I do not have a generic template for this as it would imply implementing BEP002 (Model Specification) but you can manually add modules spm.stats.fmri_spec, spm.stats.fmri_est and spm.stats.con at the end of pipeline_participant.m. Let me know if this is not clear.

Best regards,

Thank you very much! The updated version works fine!