Preprocessing

Using data collected on a Siemens Skyra 3T, we convert DICOMS to NIFTI, organize data into BIDS format, use MRIQC for quality analysis, and run fMRIprep for minimal preprocessing.

The following commands are given as an example for subject number 30000.

Download raw scan data from Osirix

The directory containing raw scan data should be moved to /Volumes/schnyer/Aging_DecMem/Scan_Data/RAW.

BIDS conversion

1. BIDS conversion with Heudiconv

CURRENTLY TESTING

docker run --rm -it -v /Volumes/schnyer/Aging_DecMem/Scan_Data:/base nipy/heudiconv:latest -d /base/RAW/Adm-{subject}/*/*/*.dcm -o /base/BIDS/ -f convertall -s 30000 -c none --overwrite

2. Convert fieldmaps

sh bids_conversion/fix_fmaps.sh

3. BIDS Validator Upload the BIDS directory to the BIDS Validator website and check to make sure there are no errors.

mriqc

Requires Docker.
Documentation available here.

To run mriqc:

Participant level command
Currently using a fd threshold of 0.25 mm for rsfMRI and 0.50 mm for task fMRI

docker run -it --rm -v /Volumes/schnyer/Aging_DecMem/Scan_Data/BIDS/:/data:ro -v /Volumes/schnyer/Aging_DecMem/Scan_Data/MRIQC/:/out poldracklab/mriqc:0.9.10 /data /out participant --fd_thres 0.25 --no-sub -vvv --participant_label 30000 

Group level command

docker run -it --rm -v /Volumes/schnyer/Aging_DecMem/Scan_Data/BIDS/:/data:ro -v /Volumes/schnyer/Aging_DecMem/Scan_Data/MRIQC/:/out poldracklab/mriqc:0.9.10 /data /out group -m {T1w,bold} 

Update excel sheet with information about scan quality

Review group mriqc report and copy values to the Google Sheet, which is available at /Volumes/schnyer/Aging_DecMem/Scan_Data/AgingDataProgress.xlsx

fmriprep

Requires Docker.
You will need to specify the path to a freesufer license file. If you do not already have a freesurfer license, you can obtain one here.

Installation instructions

To install fmriprep:

pip install --user --upgrade fmriprep-docker

To run fmriprep:

export FS_LICENSE=/Users/PSYC-mcm5324/Applications/freesurfer/license.txt
fmriprep-docker /Volumes/schnyer/Aging_DecMem/Scan_Data/BIDS/     /Volumes/schnyer/Aging_DecMem/Scan_Data/BIDS/derivatives/fmriprep/     participant -w Volumes/schnyer/Aging_DecMem/Scan_Data/BIDS/derivatives/ --notrack --ignore slicetiming -v --participant_label 30000