asl_file will just do the subtraction of tag and control images, so the output will be in the same units as the original data. If you want to normalise that by the control image you can ask asl_file to extract the control images and take the mean and then use fslmaths to do the division (for asl_file use the --spairs option with the --mean output operation and then use the image produced with _even (assuming your first volume is tag) appended to the name). Just yesterday I updated the FSL help pages to include more information on asl_file see: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/asl_file
If you are going as far as normalising by the control image, you might want to go one step further and use the formula in the ‘white paper’(1) to get your data approximately into absolute units.

Michael

1. Alsop, D. C. et al. Recommended implementation of arterial spin-labeled perfusion MRI for clinical applications: A consensus of the ISMRM perfusion study group and the European consortium for ASL in dementia. Magn Reson Med (2014). doi:10.1002/mrm.25197

On 6 Jan 2015, at 22:18, Ishtiaq Mawla <[log in to unmask]> wrote:

Hi experts,

I am trying to figure out the units on the tag-control relative perfusion image, created through --diff by asl_file. How is this computation done? What we have done before is calculate a "percent signal change" by taking the average of all control images, average of all tag images (for each voxel) then compute (avg. control minus avg. tag) divided by avg. control multiply by 100 to get the relative perfusion in % signal change units. Just wondering how asl_file did the computation and how/if I can get % signal change through asl_file.

Thanks,
Ishtiaq M.
Massachusetts General Hospital

---
Michael Chappell MEng DPhil
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Associate Professor, Institute of Biomedical Engineering, University of Oxford.
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Director of Training, EPSRC-MRC CDT in Biomedical Imaging
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Governing Body Fellow, Wolfson College, Oxford.
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Research Fellow, FMRIB Centre
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