Turns out with this approach, some parts of the brain get chopped off.
That is after you do the BET whit bias-corrected results, it also cuts
gray matter with the process of skull stripping.
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
Behalf Of Rolf Heckemann
Sent: Friday, July 31, 2009 4:19 PM
To: [log in to unmask]
Subject: Re: [FSL] fast - restore image
The command for premasking is
standard_space_roi infile outfile -b
On Fri, Jul 31, 2009 at 11:37:00PM +0100, Mojabi, Pouria wrote:
> 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
> -----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
> 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
> 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
> > them. I used fast 4 with default parameters to generate restore
> > images. Comparing the original images with the restored one, I
> > that the intensity values of restored images are much smaller
> > 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
Rolf A Heckemann, PhD
Division of Neuroscience and Mental Health
MRC Clinical Sciences Centre
Imperial College London
Hammersmith Hospital Campus
Du Cane Road
London W12 0HS