mriconvert: FSL/Nifti output and Minnesota multiband -- IMPORTANT!!

[Jolinda Smith]

Hi everyone,

A quick but important note regarding the FSL/Nifti output of MRIConvert and the multiband epi from Minnesota. First a review: MRIConvert has two options for nifti output: regular and FSL/nifti. This was necessary in the early days of nifti, until FSL fully supported the format. One important difference between the two is that "regular" nifti keeps the data in the same representation as the original dicom (typically unsigned 16 bits for MR). FSL did not support unsigned 16 bit data, but did support signed 16 bit data. Since MR images typically only use the first 12 bits, MRIConvert calls it signed 16 bits for the FSL/nifti version.

HOWEVER, the multiband sequence from Minnesota uses the full 16 bit dynamic range, so this conversion is no longer safe. I'm waiting to hear back from the FSL mailing list regarding whether FSL now supports unsigned 16 bit data. If it does, we will eliminate the FSL nifti variant, as it's no longer necessary. If it doesn't, we'll convert data that uses all 16 bits to float.

Until that happens, you have two choices if you are using FSL & the Minnesota multiband sequence:

1. Use fsl/nifti output, and check the range of your data. You can do this with fslstats filename -R. If your minimum value is 0 or higher, and your maximum is less than 32768 (and it will be if you are using fsl/nifti output), you are safe to continue as before. You'll need to do this for every file.

2. Use nifti output, and change the datatype to float: fslmaths input_file output_file -odt float.

I will keep everyone posted on further developments.

Jolinda


-- 
Jolinda Smith, Ph.D.
MR Physicist
Lewis Center for Neuroimaging
University of Oregon
Eugene, OR USA