I wrote a script to do that. Maybe this will work for you.
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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Dorian P. [[log in to unmask]]
Sent: Friday, December 20, 2013 10:38 PM
To: [log in to unmask]
Subject: [FSL] Exclude diffusion slices from analysis
Dear FSL list,
I have some DTI data with random collapsed slices. I have marked these slices for every subject. Is there a way to exclude them from DTI analysis (bedpostx, probtrackx, dtifit, etc).
Thank you and happy holidays.
Dorian
TJU
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