It may be that the window is changing and that is why you think the image is
bias corrected. In FSLView make sure the min and max have the same setting
in both the original and the extracted brains.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Steve Smith
Sent: Wednesday, August 29, 2007 8:31 AM
To: [log in to unmask]
Subject: Re: [FSL] BET
BET doesn't do bias field correction - the output can only be a
masked version of the input; the intensities are either unchanged, or
zeroed!
Cheers.
On 29 Aug 2007, at 13:19, Evangelou, Iordanis (NIH/NINDS) [F] wrote:
> Hi Steve
>
> Sorry for not being clear.
>
> I do get the extracted brain and brain mask but the extracted brain
> is not the original image fed but a new one bias field corrected.
> Is there a way to not get the bias field corrected by default. What
> i do now is multiply the original volume by the mask using fslmaths
> to get the original volume stripped.
>
> Thanks in advance.
>
> Jordan
>
> -------------------------------------------------------
> Iordanis E. Evangelou, DPhil
> Postdoctoral Fellow
> Neuroimmunology Branch
> National Institute of Neurological Disorders and Stroke
> National Institutes of Health
> Bethesda, MD 20892
> -------------------------------------------------------
>
>
>
> -----Original Message-----
> From: Steve Smith [mailto:[log in to unmask]]
> Sent: Wed 8/29/2007 12:24 AM
> To: [log in to unmask]
> Subject: Re: [FSL] BET
>
> Hi,
>
> I'm afraid I can't work out what you're asking. BET outputs a brain-
> extracted version of whatever you feed into it......?
>
> Cheers.
>
>
> On 28 Aug 2007, at 17:26, Evangelou, Iordanis (NIH/NINDS) [F] wrote:
>
>> Hi all
>>
>> We have just installed new FSL 4.0 on our Linux machines and when
>> running the following command on our (b=0) volumes
>>
>> bet b0 b0_brain -m -o -f 0.2 -g -0.1
>>
>> we see that the image is the intensity inhomogeneity corrected. Is
>> there any way to get the original image stripped?
>>
>> Thanks in advance
>>
>> Jordan
>>
>> -------------------------------------------------------------------
>> Iordanis E. Evangelou, DPhil
>> Postdoctoral Fellow
>> Neuroimmunology Branch
>> National Institute of Neurological Disorders and Stroke
>> National Institutes of Health
>> Building 10, Room 5B16
>> Bethesda, MD 20892
>> USA
>> -------------------------------------------------------------------
>>
>>
>> From: Ethan J [mailto:[log in to unmask]]
>> Sent: Tuesday, August 28, 2007 11:48 AM
>> To: [log in to unmask]
>> Subject: [FSL] how to interpret randomise -T results?
>>
>> Hello,
>>
>> I have a set of TBSS results for 14 subjects. After running the
>> randomise option to evaluate correlations of FA with some
>> behavioral measure, I am trying to make sense of the results. I
>> used the TFCE option and I have two sets of TFCE outputs -
>> tbss_tfce_tstat1 & tbss_max_tfce_tstat1.
>> How do I interpret these results? For the tbss_max_tfce_tstat1, the
>> values represent FWE corrected p values? So should I used the
>> regular min 0.949 max 1 setting to interpret my results?
>> Wht do the voxel values in the tbss_tfce_tstat1 mean?
>>
>> Thanks,
>> EJ
>>
>> Be a better Globetrotter. Get better travel answers from someone
>> who knows.
>> Yahoo! Answers - Check it out.
>
>
> ----------------------------------------------------------------------
> --
> ---
> 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
> ----------------------------------------------------------------------
> --
> ---
------------------------------------------------------------------------
---
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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