cortex.align.automatic(subject, xfmname, reference, noclean=False, bbrtype='signed', pre_flirt_args='', use_fs_bbr=False)[source]

Create an automatic alignment using the FLIRT boundary-based alignment (BBR) from FSL.

If noclean, intermediate files will not be removed from /tmp. The reference image and resulting transform called xfmname will be automatically stored in the database.

It’s good practice to open up this transform afterward in the manual aligner and check how it worked. Do that using the following (with the same subject and xfmname used here, no need for reference): > align.manual(subject, xfmname)

If automatic alignment gives you a very bad answer, you can try giving the pre-BBR FLIRT some hints by passing ‘-usesqform’ in as pre_flirt_args.


Subject identifier.


String identifying the transform to be created.


Path to a nibabel-readable image that will be used as the reference for this transform. Usually, this is a single (3D) functional data volume.

nocleanbool, optional

If True intermediate files will not be removed from /tmp (this is useful for debugging things), and the returned value will be the name of the temp directory. Default False.

bbrtypestr, optional

The ‘bbrtype’ argument that is passed to FLIRT.

pre_flirt_argsstr, optional

Additional arguments that are passed to the FLIRT pre-alignment step (not BBR).

use_fs_bbrbool, optional

If True will use freesurfer bbregister instead of FSL BBR.

save_datbool, optional

If True, will save the register.dat file from freesurfer bbregister into freesurfer’s $SUBJECTS_DIR/subject/tmp.

Nothing unless noclean is True.