Mrmetric outputs -nan!

1

Hello all,

What could go wrong if the mrmetric outputs -nan? This happens with some of my FA maps so I’m guessing something should be wrong with FA maps.
For one of the FA maps that even gives -nan when I compare it to itself (image1 and image2 are the same FA map), the mrstats output is as follows:

mrstats FA.templatespace.mif
      volume       mean     median      stdev        min        max      count
       [ 0 ]  0.0247897          0  0.0743169  -0.094143    1.04482    1965849

I appreciate any hints that help me figure out what is going wrong here.

Thank you,
Mahmoud

2

Which metric and space did you use? Voxel-space operations can become NAN if any voxel is nan, the others should not. Do you have NANs in the image? (mrcalc FA.templatespace.mif -finite - | mrstats -)

Have you tried giving FA.templatespace.mif as image1 and image2 to mrmetric?

3

Hi Max,

Thanks for your advice. I’m running the following command:

cc=`mrmetric -mask1 ${mask1} -mask2 ${mask2} ${image1} ${image2} -quiet`

Please see below:

$ mrcalc FA.templatespace.mif -finite - | mrstats -
mrcalc: [100%] computing: finite (FA.templatespace.mif)
      volume       mean     median      stdev        min        max      count
       [ 0 ]   0.999984          1 0.00397099          0          1    1965880
$ mrcalc FA.templatespace.mif -isnan - | mrstats -
mrcalc: [100%] computing: isnan (FA.templatespace.mif)
      volume       mean     median      stdev        min        max      count
       [ 0 ] 1.5769e-05          0 0.00397099          0          1    1965880

Also,

$ mrmetric -mask1 dwi_mask_in_template_space.mif -mask2 dwi_mask_in_template_space.mif FA.templatespace.mif FA.templatespace.mif
mrmetric: [100%] preloading data for "FA.templatespace.mif"
mrmetric: [100%] preloading data for "FA.templatespace.mif"
-nan

Thank you,
Mahmoud