NIFTI-1 Data Format and Orientation Conventions

FSL now uses the new NIFTI-1 data format by default, though it can still read and write "old" Analyze files. The options are:

  • ANALYZE - traditional .hdr and .img file pair (header information and image data respectively) using the ANALYZETM 7.5 file format
  • ANALYZE_GZ - same but the files are written to disk already compressed using the gzip library (saves disk space)
  • NIFTI_PAIR - the new NIFTI-1 format, still using a .hdr and .img file pair for each 3D/4D image
  • NIFTI - the NIFTI-1 format but in a single .nii file (which has the header information at the start of the file, followed by the image data)
  • NIFTI_GZ & NIFTI_PAIR_GZ - as above but with files written to disk already compressed.

    By default, FSL programs use the NIFTI_GZ format, i.e. single-file NIFTI-1 compressed images. You control which data format FSL programs write using FSL setup files (see downloading and installing for more details).

    FSL can automatically read any of the above formats, regardless of what output type has been set. However, FSL programs will generally complain and quit if you have an input image present in more than one format - for example, fmridata.hdr/fmridata.img and fmridata.nii.gz present in the same directory. If you want to bypass this safety-checking you can set the environment variable FSLMULTIFILEQUIT to FALSE (see above on FSL setup files).

    NIFTI allows the left-right orientation of your data to be specified but we do not recommend using anything but radiologically ordered images with this release. Note that avworient -getorient allows you to see the orientation stored in the header (as does avwhd). FSL treats all Analyze images as being radiologically ordered.

    You can change orientation by re-ordering the data with avwswapdim or by changing the header info with avworient.

    FSLView always shows images in radiological convention.

    Flirt can now swap the left-right orientation if the input images have different conventions. avscale now reports whether the left-right orientation is either "preserved" or "swapped" by a transformation matrix. Again we do not recommend using anything but radiologically ordered images with this release. If only radiologically ordered images are used then Flirt will not swap left-right (as was its previous behaviour).

    All previous FSL-derived images and transform matrices (including those generated by FEAT) are fully compatible with this new FSL version.

    NIFTI "sform" information (when present) is copied from the reference image when using Flirt to calculate or apply a registration.

    NIFTI "qform" information (should be) transformed from the input image and not copied from the reference image.

    All other programs should preserve the sform and qform information (or arbitrarily take it from one input if it is a process that combines many inputs)

    avwcpgeom can be used to copy this info (plus voxel dims) from one image to another.