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FSL  August 2009

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Subject:

Re: fast - restore image

From:

Rolf Heckemann <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Sat, 1 Aug 2009 00:18:32 +0100

Content-Type:

multipart/signed

Parts/Attachments:

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text/plain (84 lines) , signature.asc (84 lines)

The command for premasking is

  standard_space_roi infile outfile -b

HTH

Rolf


On Fri, Jul 31, 2009 at 11:37:00PM +0100, Mojabi, Pouria wrote:
> Hi,
>
> This is pretty useful, thank you.
> Although I can't figure out how to do the pre-mask thing with bet2
> The -b option doesn't seem to work.
>
> How do you pass that through the command line?
>
> Thank you very much
>
> -P
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Rolf Heckemann
> Sent: Friday, July 31, 2009 9:49 AM
> To: [log in to unmask]
> Subject: Re: [FSL] fast - restore image
>
> Jian
>
> fast works better on bet-processed images, but bet works better on
> images that have been bias-corrected, especially if you're dealing
> with 3-Tesla images. If you can spare the CPU cycles, a solution is
> to pre-mask with standard_space_roi -b, bias-correct the result (use
> --nopve to save time), run bet on the _restore image and bias-correct
> again.
>
> Rolf
>
>
> On Fri, Jul 31, 2009 at 04:43:28PM +0100, Jian Lin wrote:
> >
> > Hi,
> > I have T1 images (3DMPRAGE) and want to do bias field correction to
> > them. I used fast 4 with default parameters to generate restore
> > images. Comparing the original images with the restored one, I
> found
> > that the intensity values of restored images are much smaller than
> the
> > original ones, (one half or even smaller). Is it right?
> > Bye the way, I ask another question-- Do we need to do bias field
> > correction to the images before using bet or flirt?
> > Thanks a lot for your help.
> > Jian
>
> --
> Rolf A Heckemann, PhD
> Research Associate
> Division of Neuroscience and Mental Health
> MRC Clinical Sciences Centre
> Imperial College London
> Hammersmith Hospital Campus
> Du Cane Road
> London W12 0HS
> United Kingdom
> 1249058491

--
Rolf A Heckemann, PhD
Research Associate
Division of Neuroscience and Mental Health
MRC Clinical Sciences Centre
Imperial College London
Hammersmith Hospital Campus
Du Cane Road
London W12 0HS
United Kingdom
1249082071


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