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:

Monospaced Font

LISTSERV Archives

LISTSERV Archives

FSL Home

FSL Home

FSL  August 2009

FSL August 2009

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: FAST segmentation problems

From:

Yannis Paloyelis <[log in to unmask]>

Reply-To:

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

Date:

Thu, 13 Aug 2009 01:52:47 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (101 lines)

Dear Mark,
thanks so much for your super fast responses! Your help is greatly
appreciated by an FSL/structural data processing newbie like me :)

To make sure I understand, would you mean to do the segmentation in native
space, and then use FLIRT and an estimated affine matrix to bring the tissue
images to MNI space, e.g. using the command:
flirt -in tissue_image -ref refvol -out tissue_image_in_MNI -init
invol2refvol.mat -applyxfm?

On another note:
I am also interested in using priors with FAST to get a better tissue map
for basal ganglia, using the -a -P options. Would you have any comments on
the use of priors? (I trace structures on images transformed to MNI space,
and want the segmented tissue images in MNI space to feed them to a machine
learning program, along with the traced structures, to facilitate automatic
recognition).

Briefly, these are the steps I am thinking of following - please do let me
know if I do something stupid or if you have any other comments:

1. Feed axial Analyze T1s to a series of BETs to get brains (I have found
that using a two stage procedure, with [i] -S -f 0.4 and then [ii] -f 0.4
works pretty well in most cases in totally preserving the brain while
removing all the rest).
2. Use FLIRT (9 dof) to get an affine matrix to MNI space.
3. Do FAST: [a] to get a bias-corrected brain image
3. Use FLIRT to get the bias corrected brain to MNI space (the idea being
that registration may work better with bias corrected images) AND to obtain
an affine matrix.
4. Do FAST to get segmented tissue in native space, using priors -a -P, with
the affine matrix from [3].
5. Use FLIRT with segmented tissue images from [4], and apply the affine
matrix from [3] to get the segmented tissue to MNI space too.

Thanks so much for your help!

Best wishes,
Yannis

On Wed, 12 Aug 2009 19:51:41 +0100, Mark Jenkinson <[log in to unmask]> wrote:

>Hi,
>
>I think you've answered your own question.
>It is step (e) which is the problematic one.
>
>We always recommend doing segmentation in the native image
>space, as transforming to another space involves interpolation
>which blurs the intensities, making the distinctions between
>tissues less clear and the histogram less well defined.
>So just avoid the resampling, do your segmentation in the
>native space and resample your resulting segmented images
>if you want them in a different space.
>
>All the best,
> Mark
>
>
>On 12 Aug 2009, at 19:28, Yannis Paloyelis wrote:
>
>> Dear FSL users,
>>
>> Problems galore!
>>
>> I get FAST segmentation problems. When I specify:
>>
>> [1]fast -g -b -B -o output_image -p input_image (input_image=a
>> standardised to
>> MNI, brain only, T1.nii.gz), I get the message:
>> Exception: Not enough classes detected to init KMeans.
>>
>> Following from this, when I specify:
>> [P1] fast -g -a (matrix from FLIRT) -b -B -o output_image -v -p
>> input_image
>> (using prior to initialise parameter estimation) OR
>> [P2] fast -g -a (matrix from FLIRT) -b -B -o output_image -P -v -p
>> input_image (using priors throughout)
>>
>> I get the problematic images I have attached. I have checked the input
>> images and they are fine (previous steps: (a)ANALYZE T1(original) ->
>> (b)NIFTI-> (c)fslswapsim-> (d) bet-> (e)FLIRT). I get the same
>> exception
>> message even when, regarding the input image, I omit steps (c), or
>> even
>> steps (b) AND (c).
>>
>> HOWEVER, command [1] works fine (and [P1] has done so previously)
>> when the
>> input image has not been through FLIRT (i.e. step (e) was omitted,
>> and the
>> input image to FAST is not registered to MNI).
>>
>> Any ideas of what I may be doing wrong?
>>
>> Thanks so much for your help!
>>
>> Best,
>> Yannis
>> <X_gm_stdspace.jpg.zip><prob_1.jpg.zip><P2.jpg.zip>

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
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


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

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