cbf module computes the mean CBF and CBF timeseries by subtracting label-conttol pairs and modeled by the kinetic model. The module requires some parameters to be specified and standard parameters are supplied if those parameters are not provided.


Volume label The cbf_first_tagged identifies which pair of volume is label or control volume. If `cbf_first_tagged is 1, that means the first of pair volume is label and the second is control and vice versa.:

# the first volume is label

# the first volume is control


Labelling approach methods.

As of now, only two popular label strategies are implemente in xcpEngine .:

# for pulsed ASL (PASL)

# for pseudio-continous ASL (CASL/PASL)

PASL is default if none is supply.


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, cbf_m0_scale is set to 1, and average control volume is used as reference:

# scale


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


cbf_pld, cbf_tau

These two parameters are applicable to only CASL/PCASL. the cbf_tau is the label duration and cbf_pld is the post

labeling delay time. Both are expressed in seconds.:


cbf_t1blood, cbf_alpha

cbf_t1blood is the longitutdinal relaxation time of the blood in seconds and the standard value denpends 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 cbf_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.:

cbf_t1blood[cxt]=1.65 # for 3T MRI
cbf_alpha[cxt]=0.85 # for PCASL

Expected output

The main outputs are::
  • prefix_cbf.nii.gz # mean cbf
  • prefix_cbf_ts.nii.gz # cbf time series
  • prefix_cbfR.nii.gz # relative mean cbf
  • prefix_cbfZ.nii.gz # zscore mean cbf
  • prefix_sub-1_cbf_tsnr.nii.gz # temporal signal to noise ratio of cbf