Using skip skull stripping in fmriprep - where to put skull-stripped T1 files

[Steven]

Hi @fareshte

@fareshte

Apologies for missing the template info. The data was formatted according to a validatable standard. I’m not sure where to find the output of the validator though to include here.

BIDS validation should be the first thing fmriprep does, and the validation report should be at the top of your output log.

@fareshte

Could you link me to the documentation on what the rec-XX label should be?

It can be something like rec-skullstrip. As noted in the specification, the filename must be something like:

sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>][_part-<mag|phase|real|imag>]_bold.nii[.gz]/json

You won’t need all the labels, but the order of the ones you do choose must abide by that.

@fareshte

to confirm, I should add the --bids-filter-file flag in my command? Would you be able to give an example of what the input should look like?

Yes it would be part of your command, and the argument for that flag should link to a filter file you make. This part of documentation should be helpful..

Some other things:

@fareshte

    -v /Users/neurouser1/Documents/MSFatigue/Nifti/bids_directory/:/data \
    -v /Users/neurouser1/Documents/MSFatigue/xcp/fmriprep_out/:/out \

Typically the output for these pipelines should go to $BIDSROOT/derivatives

@fareshte

--mem 250GB

I doubt you will need that much memory.

Best,
Steven