Mrconvert - How to preserve intensity

2

Hi Leandro

Maybe I can provide some pointers

  1. I can’t rule out some sort of display issue from your screenshots, but are you able to check that the actual data values are indeed different? Also check that you’re looking at the same data volumes: from your command -coord 3 1:20, here image indexing starts at 0, so 1 corresponds to the second volume of the input image. With diffusion images it’s expected that some of the volumes (the b=0 ones) will have much higher intensities than the volumes with diffusion weighting (e.g. b=1000). mrconvert should certainly not be messing with the intensity values!

  2. Not as far as I know… But if it helps, you can string together multiple ranges to make things a bit easier. E.g. if you want to remove the 2nd (index 1) and 6th (index 5) volumes that would be -coord 3 0,2:4,6:end

  3. Do you mean that the output bvecs are lower precision than the input? That does seem unexpected. Maybe this thread will help? Otherwise I pass this question on to the powers that be…

Side note, you shouldn’t have to pipe together multiple mrconvert commands. It can handle multiple operations at once! like this:

mrconvert dwi.nii.gz -fslgrad dwi.bvec dwi.bval -coord 3 1:20 -export_grad_fsl fsl_bvecs.bvec fsl_bvals.bval dwi_good.nii.gz -force

Fiona

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