What image format does FSL need?
FSL programs expect to read Analyze (AVW) or NIFTI-1 format images. These files can be read and written in compressed (gzip format) or uncompressed form. To convert between these different formats, use the fslchfiletype utility or the environment variable FSLOUTPUTTYPE. These are described more fully in the nifti1 page. An image can be 2D or 3D or 4D (multiple time points). FSL programs for FMRI analysis use single 4D Analyze/NIFTI images, not lots of 3D images (such as SPM does). You will need some other program to convert between formats (e.g. DICOM). A list of such converters can be found at: www.sph.sc.edu/comd/rorden/mricron/dcm2nii.html • How do I convert between 3D and 4D Analyze images? In order to convert between multiple 3D and single 4D images, use the following programs (found in $FSLDIR/bin): 3D -> 4D     fslmerge -t outputname in1 in2 ……. inN note that if your 3D files have numbers that are zero padded (eg in0001 etc.) then you can do this more easily. For exa
