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You can use fast -B <image> to output
the B1 bias field corrected image.
Peace,
Matt.
From:
Sent: Monday, September 06, 2010
3:13 PM
To: [log in to unmask]
Subject: Re: [FSL] First - Fast
Field Inhomogeneity
Thanks Matt
I am referring to the B1 field inhomogeneity (not b0) that leads to a higher
"intensity" at the occipital cortex in my MPRAGE files. I am guessing
this is what is termed a "signal intensity bias." Does FAST have an
option that I can execute in the command line to correct this?
Cheers
From: Matt Glasser
<[log in to unmask]>
To: [log in to unmask]
Sent: Mon, September 6, 2010
3:59:01 PM
Subject: Re: [FSL] First - Fast
Field Inhomogeneity
Are you referring to b0 inhomogeneity or signal intensity bias? I don't
think it is common to have significant distortions from b0 inhomogeneity in
MPRAGE scans, but FAST can be used to correct for signal intensity bias.
Peace,
Matt.
-----Original Message-----
From:
Of Forrest Johnson
Sent: Monday, September 06, 2010 2:27 PM
To: [log in to unmask]
Subject: [FSL] First - Fast Field Inhomogeneity
Hello FSL Experts,
I am currently attempting to pull out hippocampal volumes using FIRST and
would like to correct for field inhomogeneities in my MPRAGE files prior to
running FIRST. That said, I was wondering what tool would be best to use for
this type of correction (FAST?, SUSAN?, or BET?). After sifting through the
forum I have been able to find several replies stating that applying SUSAN
is not necessary, while other replies state that FAST or BET (-B) might be
the best tools to use. Given this information I was wondering if someone
could answer the following questions
1. What is the best tool to use to correct for field inhomogeneities in my
MPRAGE?
2. Should I apply this tool before or after I bet my MPRAGE?
3. Would this order of operation be correct?
a. Correct for field inhomogeneity
b. Bet
c. first_flirt
d. run_first
e. first_boundary_correct
f. pull out volumes using fslstats
g. Apply Sienax to calculate ICV (using
VSCALING factor)
Cheers!