How do I choose fmriprep options?

Hi, Im struggling to adjust options for fmriprep.

As Im seeing couple of research paper, they are not adjusting options rather they are just using fmriprep itself.(I mean, they are not adding many options).

I wonder if there is any particular guideline about using options, like I need to use --longitudinal flag in case A, I shouldn’t use --fs-no-reconall flag in case B.

If there are, please lemme know.

Junyong Oh.

Hi @dhwnsdyd21 , the idea of adding options to fmriprep is to be able to adjust the processing pipeline to most of the researchers tastes and data.
In fact fmriprep is calling many tools (ANTs, FreeSurfer, FSL …) and for each operation, there are often many options.

In general the default options work well, but you may want to get your output in a specific template space, in that case you can use the --output-spaces option for instance. This is just an example.

--fs-no-reconall is not recommended anymore (see this discussion )