Hi Christian,

FSL comes with 'slicer'. You can do this:

slicer /usr/share/data/fsl-mni152-templates/MNI152_T1_2mm.nii.gz -y 0.5 test.png

and test.png will contain the mid-axial slice. But it can do more:


Usage: slicer input [input2] [main options] [output options - any number of these]

Main options: [-L] [-l ] [-s ] [-i ] [-e ] [-t] [-n] [-u]
These must be before output options.
-L       : Label slices with slice number.
-l : use a different colour map from that specified in the header.
-i : specify intensity min and max for display range.
-e : use the specified threshold for edges (if >0 use this proportion of max-min, if <0, use the absolute value) 
-t       : produce semi-transparent (dithered) edges.
-n       : use nearest-neighbour interpolation for output.
-u       : do not put left-right labels in output.

Output options:
[-x/y/z ]      : output sagittal, coronal or axial slice
     (if >0 it is a fraction of image dimension, if <0, it is an absolute slice number)
[-a ]                  : output mid-sagittal, -coronal and -axial slices into one image
[-A ]          : output _all_ axial slices into one image of _max_ width
[-S ] : as -A but only include every 'th sliceCheers,Michael