Oxford_ASL is an automated command line utility that processes ASL data to produce a calibrated map of resting state tissue perfusion. Typical usage would be:

oxford_asl -i <asl_data> -o <output_dir_name> --tis=3.2 --bolus=1.8 --casl

This command would process the data specified by <asl_data> which has contains multiple volumes of tag-control difference images from a pcASL (pseudo-continuous labelling) acquisition with inflow-time 3.2 s (post labelling delay 1.8 s) and labelling duration 1.8 s. this data may for example have been acquired using the recommendation from the ASL consensus paper: Alsop et al., MRM, 2014. It would calculate a relative perfusion map using an inversion of the standard ASL kinetic model with the default parameters specified in oxford_asl.

oxford_asl -i <asl_data> -o <output_dir_name> -s <struct_image> -t <struct2std_trans.mat> -c <M0_calib_image> --tr=5 --tis=0.2,0.4,0.6,0.8,1.0,1.2,1.4,1.6,2.0,2.2

This command would process the data specified by <asl_data> that has been acquired with a pASL (pulsed labelling) acquisition that contains multiple volumes of tag-control difference images with the list of inflow-times (inversion-times) --tis. The resulting tissue perfusion map would registered into standard space by way of the structural image <struct_image> and structural to standard transformation matrix <struct2std_trans.mat>. Finally a calibrated perfusion map (in ml/100g/min) would be produced using the calibration image <M0_calib> (a proton density weighted image with TR of 5 s) using CSF as a reference to calculate the equilibrium magnetisation of blood within an automatically generated CSF mask (from a segmentation of the structural image). Results are provided both in the native space of the original perfusion image, as well as in standard space (in case the registration needs to be revisited later).

When a structural image is supplied Oxford_asl will try to register the resulting CBF image to the structural image. It is very important to inspect whether the registration has worked by examining the final result. In practice the current default registration is only robust for some forms of ASL data. There are a couple of options that can improve the robustness of registration (see below). Advanced custom registration can be done using the native_space results directly and either asl_reg or flirt.

Changes from FSL 5.0.6 onward

Oxford_asl was modified in FSL 5.0.6 to make it more consistent with the ASL consensus paper. Thus T1 values differ from the earlier releases and the inversion efficiency is now included by default (this can be 'turned off' by setting --alpha=1) - the new defaults for these can be found by typing oxford_asl on the command line and consulting the usage information. Oxford_asl now also expects all structural images to have already been brain extracted (in the past bet was run internally). This now leaves it up to the user to choose their preferred bet options and get the brain extraction they wish without any further modification by oxford_asl.


The outputs from Oxford_ASL are a resting state perfusion image called perfusion.nii.gz, which provides blood flow in relative (scanner) units, and, fi data at multiple inflow-times is supplied, an arrival time image called arrival.nii.gz. If calibration has been requested then a further image perfusion_calib.nii.gz is also produced, which is a flow map in absolute units (ml/100g/min).

If calibration was performed using a CSF reference then a text file called M0b.txt will be created that saves the estimated M0 value from arterial blood. If a CSF mask was not supplied then the automatically generated one (from segmentation of the structural image) will also be saved in the output directory as csf_mask.nii.gz. It is good practice to examine this to ensure that any voxels in the mask are well within the CSF of the low resolution ASL images.

A subdirectory is always created called native_space in which perfusion and arrival time images in the native resolution of the ASL data are saved. These are useful if you find the registration to be unsatisfactory, allowing a new registration to be performed without having to repeat the main analysis.

Main options

Typing oxford_asl with no options will give the basic usage information, the following is a more detailed version.

Some options are only present in more recent releases of oxford_asl

acquisition specific

At the very least you need to specify the inflow-time(s) (inversion times for pASL, bolus duration plus post-labelling delay of pcASL) for the data acquisition along with the labelling strategy (pASL or pcASL) and bolus duration (label duration).

Structural image

The structural image is used as a reference for registration, to generate a CSF mask for absolute quantification (if called for) and to provide partial volume estimates for correction of perfusion for partial volume effects (if requested). The bias field from the structural image may also be used to correct for coil sensitivity variations.


By default oxford_asl will generate perfusion (and arrival time) images in the same space as the original data and also at higher resolutions if a structural image (and transformation to standard space) has bee supplied. Further detailed results and summaries can also be produced:


Using the following options it is possible to request asl_calib perform the calibration required to get the M0 of arterial blood and apply it to the perfusion images. More options are available, see the advanced options. This uses asl_calib and a custom calibration calculation can be performed using that tool.

Advanced options

A list of all the extended options (plus notes) can be found with the --more command:

oxford_asl --more


Various options exist for efine the analysis performed on the ASL data, the majority of these apply to multi inflow-time data where more options exist in the form of kinetic model to be used to quantify perfusion.

* -t (optional) [struct2std_trans.mat] transformation matrix that takes the structural image into standard space. This matrix is an output from the registration process carried out by FLRIT (this is a normal part of FEAT processing for fMRI data for a subject). If this is not supplied data will be output in structural space.


* --csf (optional) [csf_mask] Image in the same space as the structural (or low res structural image if supplied) that is a mask of voxels containing CSF to be used in calibration. This is a further option of the calibration step and allows the CSF mask to be manually specified if the automated procedure fails.



oxford_asl/UserGuide (last edited 15:57:43 22-01-2015 by MichaelChappell)