Intensity normalisation of DWI data from control and TBI rats


Dear all,

Currently I am analysing DWI data from control and TBI rats. I have a question about dwinormalise for the rat brain. I first tried to run dwiintensitynorm to perform global intensity normalisation across subjects (step 5) [after I already went through step 1 to 4]. Somehow this script failed somewhere in the process which has something to do with the registration (might be due to the shape of the rat brain, which is of course quite different from a human brain in size and shape). Therefore I did some steps manually: (1) I made my own study-specific template, (2) registered all FA images to the template, (3) created a WM mask by thresholding, and (4) projected the WM mask back into subject space. Now everything should be ready to apply dwinormalise, since it’s stated that “The mask is then transformed back into the space of each subject image and used in the dwinormalise command to normalise the input DW images to have the same b=0 white matter median value.Elsewhere on the forum (response June 2017) it’s also stated that inter-subject normalisation is provided by dwinormalise.

So I applied dwinormalise to every rat DWI image, using the ‘back projected subject specific WM mask’ as a mask and the default value of ‘1000’. To check the result, I compared the median b=0 white matter values of two rats, and they were slightly different, so they don’t have ‘the same b=0 white matter median value’ as is stated above.

So my question is, does the dwiintensitynorm script apply the dwinormalise step in a ‘special way’, e.g. by normalising every subject by it’s own median b=0 white matter value? In that case every median b=0 white matter value would be 1000 and indeed ‘the same’. How does the script deal with multiple b=0 images? May be I missed something, I just want to know if I’m on the right track, before I start with ‘Fixel Based Analysis’ (another 17 steps)… :wink:

And a related question, which might also be important for the inter-subject global intensity normalisation. We have a dataset of rats with and without traumatic brain injury (TBI). TBI causes wide spread white-matter damage, so should some steps (like normalisation or average FOD estimation) be performed separately for control and TBI rats? Or should there be one study-specific template etc.? Furthermore, data acquisition is longitudinal, similar questions here. Does anyone has experience with a similar set up?

Thanks in advance for your advice and suggestions!

Kind regards,