Scanning

Checklist

Given the time limitations, scanning day can be stressful for the operators. We strongly recommend that you make a checklist for your study and decribe the procedure step by step. This will minimize the operator errors/mistakes on the scanning day.

An example of a checklist used for an EEG/fMRI study can be found here: pdf

Data transfer

After you are done with the scans, open a Terminal and run cfmricp to transfer your data to your desired server. If your protocol includes a multi-band scan, you may need to wait 10-15 minutes after the scan to get the reconstructed data.

cfmricp will transfer the dicoms, physio recordings and the reconstructed multi-band images. It will also create a log file with the name of the scans and their associated dicom directories.

Converting to BIDS

The data that is transfered using cfmricp can be converted to BIDS format using cfmri2bids. cfmri2bids is a script written in matlab that utilizes dcm2nii and the cfmricp log file to reconstruct the data and convert them to BIDS format.

An exmple of a directory converted to BIDS:

cfmri2bids is in /data/mfalahpour/data/bitbucket_proj/bidstools repository.