Hi Matthew,
I have only been focusing on the restored
images at the moment, as I have been incorporating a bias correction step into
the preprocessing of T1 and FLAIR images. I do think that multiple
iterations of FAST give a more homogeneous output image (with respect to
bias). The old version of FAST often over corrected the bias, whereas
FAST4 tends to under correct the bias, however with subsequent iterations it
usually tends toward an (accurate) equilibrium. We tend to get very good
segmentation results except in motor cortex and in the thalamus (these are
non-human primate scans), however the contrast in these regions is poor due to
the large amount of myelin present.
Peace,
Matt.
From:
Sent: Monday, April 14, 2008 5:14
AM
To: [log in to unmask]
Subject: Re: [FSL] Fast4 Question
Hello Matt,
Thanks for the command line information. It's
possible that the differences you are seeing by rerunning with the restored
image is due to fast4's initial bias field estimation being different to that
used in the -I iterations. Hence by running twice you are getting the initial
correction applied twice ( on the original and restored images respectively). I
would be very interested if you think that running fast4 twice always gives a
better segmentation or if it's data set dependent. The --Hyper option is
just a scaling factor ( set to < 0 to auto-estimate ) the --lowpass option
is in mm.
Many Regards
Matthew
Hi Matthew,
Thanks for your reply. Here is an
example commandline applied to a T1 image:
fast4 -b -o default T1Struct
fslmaths T1Struct -mul default_bias
T1Struct_default
fast4 -b -I 8 -o I8 T1Struct
fslmaths T1Struct -mul I8_bias T1Struct_I8
fast4 -b -I 12 -o I12 T1Struct
fslmaths T1Struct -mul I12_bias
T1Struct_I12
The files T1Struct_default T1Struct_I8
T1Struct_I12 are all the same. If I run the default, and then run the
default again on the restored image I get a different (somewhat better)
result. Also, what are the units of the --lowpass and ---Hyper smoothing
options?
Thanks,
Matt.
From:
Sent: Monday, April 07, 2008 6:39 AM
To: [log in to unmask]
Subject: Re: [FSL] Fast4 Question
Hi,
We've done some tests
with fast4 and we can't replicate what you've seen with an invariant bias field
for different --iter. Could you go into more detail into the method you've used
( specific command lines etc)? Given the smaller brain size you may want to
lower the --lowpass and ---Hyper smoothing options...
Many Regards
Matthew
I have found that running
fast4, restoring the image with the bias field, and then rerunning fast4
several times gives a better estimation of the bias field than just running
fast4 a single time. I tried to duplicate this by increasing the number of
main-loop iterations during bias-field removal (the --tier option) from 4 to 8,
for example, but this gave exactly the same result for the bias field
restoration. How would I get the same improvement in bias field
estimation without rerunning the program several times (and wasting time
calculating segmentations that I don’t plan to use)? Also, are
there any settings I should change for non-human primates with their smaller
brains? It seems like sulci are often smoothed out of the segmented image.
Thanks,
Matt.