t1fit

T1 fitting algorithms based on algorithms described in "A robust methodology for in vivo T1 mapping" by Barral, Gudmundson, Stikov, Etezadi-Amoli, Stoica and Nishimura, MRM 2010. There are also routines to unshuffle slices from a slice-shuffled pulse sequence, where each slice within a volume experiences a different inversion time. (E.g., the CNI slice-shuffed SMS-EPI sequence.)

E.g., to unshuffle slices and compute T1 estimates from a NIFTI file containing slice-shuffled T1 data:

./t1_fitter -u /path/to/nifti.nii.gz

For detailed usage information, run

./t1_fitter.py -h

Correcting for EPI distortion

EPI distortion correction is done using FSL's topup tool. Provide the NIFTI file of the reversed phase encoding acquisition, along with the NIFTI file of the original phase encoding acquisition, and run the script t1fit_unwarp.py with:

./t1fit_unwarp.py -p /path/to/reverse/pe/nifti.nii.gz /path/to/nifti.nii.gz outbase

Other options include:

--cal       number of calibration volumes at the beginning of the nifti file (default=2)
--mux       number of SMS bands (mux factor) for slice-shuffled data (default=3)
--tr        TR of the slice-shuffled scan in ms (default=3000)
--ti        shortest inversion time of the slice-shuffled scan in ms (default=50)
--method    interpolation method for FSL's applytopup, 'jac' or 'lsr' (default is 'jac'). 
            Refer to FSL's applytopup for further information.

For detailed usage information, run

./t1fit_unwarp.py -h