Dear FSL expersts,
I’m trying to align my raw DTI data using FLIRT and write it out in Analyze
format.
Here is what I did: I created a single Analyze file of raw DTI data (7
volumes, 6 directions + b0), did EPI distortion correction and saved it
again as a single Analyze file. Then I opened FLIRT window, selected input
image (a single Analyze EPI-corrected file with 7 volumes), named output
image. I left all the other setting at default, including the reference
image, i.e. MNI template. I clicked on go and checked the results in MRIcro.
Here is the problem: The alignment worked fine, but the volumes got lost. I
can only open the first, b0 volume. MRIcro doesn’t ask anymore which volume
it should show (1 through 7) like it did with EPI-corrected image. It only
recognizes the first one.
Here is the question: What did I do wrong? How do I align all 7 volumes and
save them back to a single Analyze file?
I would appreciate your help.
Thank you.
Anna
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