I have a simple question here.
I have for each subject a 3D dataset which is one sub brick that contains only the beta coefficients for each voxel. I need to normalize those coefficients by a reference value which is the averaged signal across all functional volumes and voxels of each subject. (I am following a suggested pipeline to calculate a cerebro vascular reactivity index for each voxel). For each subject I have a .1D file which contains one number. (this number is different for each subject). What function can I use to divide each voxel in my sub brick dataset by this number?
I tried 3dcalc but it can only do voxel by voxel operations so it complains when I include as second input dataset which is not a 3d dataset
3dcalc -a betaCoefficients.nii.gz -b referneceValue.1D -expr ‘a/b’ >normalized betas.nii.gz
for bash: 3dcalc -a betaCoefficients.nii.gz -b -expr ‘a/$( cat referneceValue.1D)’ >normalized betas.nii.gz
for tcsh or bash: 3dcalc -a betaCoefficients.nii.gz -b -expr ‘a/cat referneceValue.1D’ >normalized betas.nii.gz
This assumes that there is one and only one properly formatted number in referneceValue.1D
Thank you very much for your help guys!
I think the -b did not belong there. Once I removed it it worked !
Thank you very much :))
Cheers
Carolin
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.