JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for FSL Archives


FSL Archives

FSL Archives


FSL@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

FSL Home

FSL Home

FSL  February 2008

FSL February 2008

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Tissue segmentation in macaques

From:

Tim Behrens <[log in to unmask]>

Reply-To:

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

Date:

Fri, 1 Feb 2008 07:35:04 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (92 lines)

Hi - just a couple of add on points.
It is probably the case that the bias field is the problem here. I  
know FAST can deal with a bias field, but
I suspect it is tuned for smaller gradients than the one you have.  
Was the data acquired with a surface coil?

Anyway, if this is true, there are several things you might try, but  
they may need a bit of playing around.
1. Significantly increase the number of iterations in fast (-i)   
( the default settings are tuned for the kind of brains Yongyue was  
used to seeing..)
2. Significantly reduce the bias field smoothness in fast (-l) - this  
will allow fast to estimate quickly changing bias fields - I suspect  
you should always do this in macaques because the brain is smaller  
and therefore the bias field will be less smooth (when measured  
absolutely).

3. Now we are really getting desperate - divide each slice by its  
mean value - you might need to do something a bit different for the  
end slices that are mostly grey matter, but this will certainly have  
a dramatic effect.


Hope these things are slightly useful

T



On 1 Feb 2008, at 02:57, Matt Glasser wrote:

> Joe,
>
> There are probably several things going on here: 1) Motor cortex  
> contains
> more myelin than other cortical areas, and as a result, T1 contrast  
> is not
> as good as other cortical areas.  2) You should use the -or and the  
> -ob
> switches of the fast utility to check that the bias correction is not
> actually making things worse at the top of the brain.  I have found  
> in some
> instances that it helps to set a lower threshold to remove any low  
> intensity
> regions around that outside of the brain that were not removed by  
> bet.  3)
> If neither of these methods work, you can improve the tissue  
> contrast by
> using fslmaths to square the image, which increases the difference  
> between
> low and high values.  You may have to set an upper threshold to  
> remove blood
> vessels, which will increase in intensity much faster than other  
> regions, to
> the point that they segment in a separate category.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On  
> Behalf
> Of Joseph T. Devlin
> Sent: Thursday, January 31, 2008 6:20 PM
> To: [log in to unmask]
> Subject: [FSL] Tissue segmentation in macaques
>
> Hi FSLers,
>
> I've been trying to use FAST to get a good grey/white segmentation of
> some monkey brains and having been running into some difficulties.
> FAST does a nice job with the ventral half of the brain but more
> dorsally, it is classifying most voxels as white matter.  Although by
> eye, there is a clear grey-white demarcation, in the more dorsal
> areas the grey matter values appear to be closer to WM values,
> especially WM values in the ventral part of the brain.  I thought
> this might be a bias field issue, but the bias field outputted by
> FAST definitely does not show a ventral-dorsal gradient.  To be
> honest, I'm not sure how this is generated, so I'm not certain what
> to make of that.
>
> Regardless, the information necessary to successfully segment GM from
> WM appears to be present in the image -- at least to my eye, the
> differences are clear and robust throughout the entire
> image.  Nonetheless, I can't seem to find a way to robustly extract
> this with FAST and would welcome any suggestions.
>
> Thanks, in advance.
>
> Joe
>

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001


WWW.JISCMAIL.AC.UK

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager