fMRIPrep

[yukaizou2015]

• Running fMRIPrep via Docker

[yukaizou2015]

docker system prune -af
docker pull nipreps/fmriprep:latest

Run: docker run nipreps/fmriprep

Incorporated into BIDS DcmSourcedata_to_NiftiRawdata.sh - Line

[finnlennartsson]

Not implemented any distortion correction?? https://fmriprep.org/en/0.5.3/workflows.html#module-fmriprep.workflows.fieldmap

Is the fmap not working?? https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#case-3-direct-field-mapping

Is there a problem could that we have not updated the .json file with "Intended for field" https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#using-intendedfor-metadata

[yukaizou2015]

Not implemented any distortion correction?? https://fmriprep.org/en/0.5.3/workflows.html#module-fmriprep.workflows.fieldmap

Is the fmap not working?? https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#case-3-direct-field-mapping

Is there a problem could that we have not updated the .json file with "Intended for field" https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#using-intendedfor-metadata

Phase-difference techniques are chosen for mapping the field (see here for details).

• Use phase-difference for now, future (recommended) switches to Blip-up/blip-down or phase encoding polarity (used to developing human connectome project)

Each subject at each session contains one phasediff.json files under fmap/. Two things need to be done to update this file:

1. Add attribute "IntendedFor".
2. Update attribute "SliceTiming" (see issue #12).

[finnlennartsson]

We may have multiple runs of . How do we chose which to use???

The solution can be to use a bids filter which controls which files that should be used by fmriprep

https://fmriprep.org/en/stable/faq.html#how-do-i-select-only-certain-files-to-be-input-to-fmriprep

[yukaizou2015]

We may have multiple runs of . How do we chose which to use???

The solution can be to use a bids filter which controls which files that should be used by fmriprep

https://fmriprep.org/en/stable/faq.html#how-do-i-select-only-certain-files-to-be-input-to-fmriprep

Now that head motion can be quickly evaluated without having to run fMRIprep, have made running docker_run_fmriprep_noFS.sh as optional. As default, run segmentation.sh first, followed by running docker_run_fmriprep_postFS.sh