All the avw commands now start with fsl. Ie. Fslroi
So. You found docs referring to the older nomenclature
Dg
------Original Message------
From: Adam Green
Sender: FSL - FMRIB's Software Library
To: [log in to unmask]
ReplyTo: FSL - FMRIB's Software Library
Subject: [FSL] avwroi for nodif_brain_mask
Sent: Dec 3, 2008 12:22 PM
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
Sent from my Verizon Wireless BlackBerry
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