Sunday, May 18, 2014

ReHo Normalization with FSL

As a brief addendum to the previous post, ReHo maps can also be normalized using FSL tools instead of 3dcalc. Conceptually, it is identical to what was discussed previously; however, the ability to set variables as the output of FSL commands makes it more flexible for shell scripting. For example, using the same datasets as before, we could set the mean and standard deviation to variables using the following combination of AFNI and FSL commands:

3dAFNItoNIFTI ReHo_Test_Mask+tlrc
3dAFNItoNIFTI mask_group+tlrc

setenv meanReHo `fslstats ReHo_Test_Mask.nii -M`
setenv stdReHo `fslstats ReHo_Test_Mask.nii -S`
fslmaths ReHo_Test_Mask.nii -sub $meanReHo -div $stdReHo -mul mask_group.nii ReHo_Norm
gunzip *.gz
3dcopy ReHo_Norm.nii ReHo_Norm

An explanation of these commands is outlined in the video below. Also, suits!

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