# basil¶

Basil module computes the CBF and the derivatives using Bayesian inference method for the kinetic model inversion. It also part of FSL and can aslo be run independently.

## basil_perfusiion¶

Labelling approach methods.

As of now, only two popular label strategies are implemented:.:

# for pulsed ASL (PASL)
basil_perfusion[cxt]=pasl

# for pseudio-continous ASL (CASL/PASL)
basil_perfusion[cxt]=casl


PASL is default if none is supply.

## basil_inputformat¶

Volume label The basil_inputformat identifies which pair of volume is label or control volume. There are three types- tc (label-control), ct(control-label) and diff (cbf).:

 # the first volume is label
basil_inputformat[cxt]=tc

# the first volume is control
basil_inputformat[[cxt]=ct

# each volume is cbf, already substracted
basil_inputformat[[cxt]=diff


## basil_spatial and basil_pvc¶

If the spatial regularization (basil_spatial) by kernel and the partial voulme correction (basil_pvc) are require, they are set to 1s or otherwise 0s

# spatial regulaization
basil_spatial[cxt]=1

# Partial volume correction
basil_pvc[cxt]=1


## basil_m0_scale¶

M0 scale.

If the M0 scan is included and acquired at different scale to ASL acquisition, the user can supply the M0 scale. if there is no M0, basil_m0_scale is set to 1, and average control volume is used as reference/M0:

# scale
basil_m0_scale[cxt]=1


## basil_lambda¶

The lambda is the blood-brain partition coefficient that scales the signal intentisty of tissues to that of blood. The common or standard value is ƛ=0.90 ml/g.:

#
basil_lambda[cxt]=0.9


## basil_pld and basil_tis¶

These are applicable to only CASL/PCASL. basil_pld is the post labeling delay time in seconds and basil_tis is the invertion time. The invetion time is the sum of label duration and post labelling delay. BASIL accepts multiple pld and tis separated by commas:

# single pld
basil_pld[cxt]=1.8
basil_tis[cxt]=3.6 # this implies label duration is 1.8 scale

# multiple plds
basil_pld[cxt]=0.25,0.5,1,1.5
basil_tis[cxt]=2.05,2.55,3.55,5.05 # this implies label duration is 1.8 scale


## basil_t1blood, basil_alpha¶

basil_t1blood is the longitutdinal relaxation time of blood in seconds and the standard value denpend on the field strength of MRI machine. For 3T and 1.5T, the standard cbf_t1blood values are 1.650s and 1.350s respectively. The basil_alpha is the labelling efficiency and values are different for PASL and CASL/PCASL. The standard value is 0.85 for CASL/PCASL and 0.98 for PASL.:

#
basil_t1blood[cxt]=1.65 # for 3T MRI
basil_alpha[cxt]=0.85 # for PCASL


## basil_MOTR¶

This is for the TR of MO scan if it is available. It is very important for the purpose of calibration and also account for shorter TR value. The default is 3.2s but it also read from the MO scan image.

## Expected output¶

The main outputs are::
• prefix_cbfbasil.nii.gz # mean basil cbf
• prefix_cbfpv.nii.gz # partial volume corrected cbf
• prefix_cbfspatial.nii.gz # spatial regularized cbf

All thier respective relative (R) and zscore (Z).