Sure, you can use it for presentations, but what threshold should we
have used? I am still unclear why the unmasked data look that way....
Also, I would expect the output of feat to show how good registration
is. If this is true, then the program is picking the wrong images to
display. Can you confirm or deny that?
Finally, if the brain mask used automatically in feat does not work, how
do I pass my own mask to the program?
Stefano Marenco, MD
GCAP, Clinical Brain Disorders Branch,
NIMH
10 Center Drive, room 4S235
Bethesda, MD 20892
tel. (301) 435-8964
fax. (301) 480-7795
email: [log in to unmask]
-----Original Message-----
From: Steve Smith [mailto:[log in to unmask]]
Sent: Thursday, November 16, 2006 8:03 AM
To: [log in to unmask]
Subject: Re: [FSL] a question about masking in fugue-feat
Hi Stefano,
This is due to a masking problem; you've turned off BET but left the %
threshold (misc tab) at 10%. By turning BET back on I get very nice
results.
This is a lovely example to show the value of FUGUE - is it ok if we
keep it and maybe use it in presentations?
Cheers.
On 10 Nov 2006, at 22:07, Marenco, Stefano (NIH/NIMH) [E] wrote:
> I sent a tar file to your website reference number 680248.
>
>
> In this acquisition, we acquired fieldmaps and used them to correct
> for epi distortion of a phantom. The epi acquisition was done with
> an 8 channel coil and the fieldmaps were acquired with the body coil.
>
> We did not use a mask b/c we thought that bet would fail with this
> phantom and because this phantom does not have a "skull"; and we
> observed the weird halo that can be seen in the
> undistorted_example_func image. Why does this happen?
>
>
> From the output of the program, it is easy to see that the
> correction was actually quite accurate (despite some overcorrection
> of distortion in the posterior section of the phantom, which I am
> not sure how to explain).
>
>
> I believe also the registration between the fieldmap and the epi
> was done correctly, however the images displayed in the second and
> third row of the output show misalignments. It is not clear to me
> why these images were chosen for an output that should show how
> good the registration was, not how far apart the original volumes
> were....
>
>
> Sometimes the automatic settings for bet fail. Since the masking
> has to be quite precise in order not to leave "halos" just around
> the cortex, would it be possible to modify the feat script so that
> one could introduce a different mask in case of failure of the
> default settings?
>
>
> Thanks again for all your help
>
>
> Stefano Marenco, MD
>
> GCAP, Clinical Brain Disorders Branch,
>
> NIMH
>
> 10 Center Drive, room 4S235
>
> Bethesda, MD 20892
>
> tel. (301) 435-8964
>
> fax. (301) 480-7795
>
> email: [log in to unmask]
>
>
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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