Skip to content

epi_reg

epi_reg is a script designed to register EPI images (typically functional or diffusion) to structural (e.g. T1-weighted) images. The pre-requisites to use this method are: (1) a structural image that can be segmented to give a good white matter boundary; and (2) an EPI that contains some intensity contrast between white matter and grey matter (though it does not have to be enough to get a segmentation).

This script will either use an existing white-matter segmentation of the structural image, or create one itself, to define a white-matter boundary. To use an existing white-matter segmentation you can use the --wmseg option. Alternatively, there needs to be an image with the same basename as the input --t1brain image, but ending with _wmseg. We recommend that the structural image is bias-corrected separately beforehand if there is obvious bias field present.

The script is also capable of using fieldmaps to perform simultaneous registration and EPI distortion-correction. For this it requires extra images (in the format as given by fsl_prepare_fieldmap) as well as extra information about the EPI sequence (which your operator/radiographer/technician should be able to provide, but make sure you record the values). The inputs --echospacing and --pedir both refer to the EPI image (not the fieldmap) and are the same as required for FEAT, but be careful to use the correct units.

Command-line usage is as follows:

Usage: epi_reg [options] --epi=<EPI image> --t1=<wholehead T1 image> --t1brain=<brain extracted T1 image> --out=<output name>

Optional arguments
  --fmap=<image>         : fieldmap image (in rad/s)
  --fmapmag=<image>      : fieldmap magnitude image - wholehead extracted
  --fmapmagbrain=<image> : fieldmap magnitude image - brain extracted
  --gdc=<image>          : Gradient-distortion corection warpfield
  --wmseg=<image>        : white matter segmentation of T1 image
  --echospacing=<val>    : Effective EPI echo spacing (sometimes called dwell time) - in seconds
  --pedir=<dir>          : phase encoding direction, dir = x/y/z/-x/-y/-z
  --weight=<image>       : weighting image (in T1 space)
  --nofmapreg            : do not perform registration of fmap to T1 (use if fmap already registered)
  --noclean              : do not clean up intermediate files
  -v                     : verbose output
  -h                     : display this help message

e.g.:

epi_reg --epi=example_func --t1=struct --t1brain=struct_brain --out=epi2struct --fmap=fmap_rads --fmapmag=fmap_mag --fmapmagbrain=fmap_mag_brain --echospacing=0.0005 --pedir=-y

Note that if parallel acceleration is used in the EPI acquisition then the *effective* echo spacing is the actual echo spacing between acquired lines in k-space divided by the acceleration factor.