AFNI Class Notes 8/16/2019:

Helpful AFNI links:

AFNI lessons:

https://afni.nimh.nih.gov/pub/dist/edu/2016_0222_lister_hill/

AFNI data example:

https://afni.nimh.nih.gov/pub/dist/edu/data/CD.expanded/AFNI_data6/

Tools discussed:

Dicom-to-BRIK/NIFTI tools:

dicom_hdr: outputs dicom information to commandline

dcm2nii: part of MRIcro package that reads header details

dcm2niix: part of MRIcroGL package that fits BIDS 

to3d: afni, defaults to AFNI but can do NIFTI.

Dimon: afni function that reads dicom header designed for real time

Distortion correction:

field map correction: FUGUE but use Keck fieldmap.html

topup correction: topup but use Keck howtoindex.html

              First Step in processing:

                              uber_subject.py: gui for creation of afni_proc.py