From: Mark Jenkinson <[log in to unmask]>
To: [log in to unmask]
Sent: Thu, August 26, 2010 4:52:44 PM
Subject: Re: [FSL] intensity normalization
You can find the C++ code for this easily in fslmaths.cc
(in $FSLDIR/src/avwutils/ )
This shows that it just excludes the zero voxels - see the code below
where the key line is the binarise with the exclusive option to form the
else if (string(argv[i])=="-inm")
target = atof(argv[++i]);
All the best,
On 26 Aug 2010, at 22:39, Kim Chi Nguyen wrote:
> I have a question about intensity normalization command: fslmaths inputVol -inm 10000 outputVol. To my understanding, that command should make the mean of each volume in the 4D inputVol to 10000. Particularly, let h be the 1st volume in the 4D
inputVol: h=inputVol(:,:,:,1) . After the normalization step, let t=outputVol(:,:,:,1). So we should have t=h.*10000/mean(h) i.e. mean(t)=10000 (mean function here denotes for 3D mean calculation).
> In fact I used that command and I also do the normalization manually in Matlab. However, the two normalization results does not match. I suspected that you only include the voxels that are greater than some certain voxels into the processing of calculating the mean and normalizing it... Am I correct? If yes, please let me know what is the default threshold that FSL uses? If not, please explain to me what I do/think wrongly here.
> Thank you very much.