Hi,
Try fslroi.
Cheers-
Andreas
-----Ursprüngliche Nachricht-----
Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Adam Green
Gesendet: Mittwoch, 3. Dezember 2008 18:22
An: [log in to unmask]
Betreff: [FSL] avwroi for nodif_brain_mask
Hi all.
I'm attempting to generate a nodif_brain_mask from my eddy corrected data in order to run bedpostx. Some google searching (and searching on this list), indicates that I should point the avwroi command at my data.nii.gz file containing the 4D DTI data like so: avwroi data.nii.gz nodif 0 1. The idea being to generate a mask from the non-diffusion-weighted zero volume, as opposed to just choosing the "output binary mask" option from a BET of my data.nii.gz file. 1) Is this the correct procedure? 2) Any suggestions about why I get the "command not found" error message when I try to run avwroi (or the other avw commands) from the command line, even after launching fsl?
Thanks for any help.
-Adam
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