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

Help for SPM Archives


SPM Archives

SPM Archives


SPM@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

SPM Home

SPM Home

SPM  October 2007

SPM October 2007

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: [FSL] sienax problem 512x512 scans

From:

John Ashburner <[log in to unmask]>

Reply-To:

John Ashburner <[log in to unmask]>

Date:

Fri, 26 Oct 2007 19:06:02 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (178 lines)

Such a 2 stage procedure is only really necessary if the deformation is 
parameterised by a small number of parameters.  If the deformations don't 
need to also model variability outside the region in which you are 
interested, then it is better able to model variability within that region.

According to my contacts within FMRIB, they are developing some nice nonlinear 
warping algorithms, which use more parameters.  When their new algorithms are 
released, then such a masking procedure should no longer be required.

Similarly, there is also a new warping procedure within SPM5.  You can access 
it via TASKS->Tools->DARTEL, and there is some documentation about how to use 
it in the man/manual.pdf file.

Best regards,
-John

On Friday 26 October 2007 17:58, Buyean Lee wrote:
> Dear Ged,
>
>
>
> I would like to ask one more similar question; can one safely use FSL
> processing in SPM5 analysis.
>
>
> For example, if one is interested in only the subcortical regions (e.g,
> volume or dopamine D2 receptors), I think one can use the following
> two-stage normalization in order to improve the accuracy of normalization
> of the subcortical regions.
>
>
> This is the description in the FSL website.
>
>
>
> "first_flirt - This script runs two-stage affine
> registration to MNI152 space at 1mm resolution (we will assume for
> these instructions that the image is named im1.nii.gz). The first
> stage is a standard 12 degree of freedom registration to the template.
> The second stage applies a 12 degrees of freedom registration using an
> MNI152 sub-cortical mask to exclude voxels outside the sub-cortical
> regions."
>
>
> I can easily observe that the normalized images by this two-stage
> registration is better fitting into the standard MNI space, if I focus on
> only the subcortical regions; but normalization of other areas such as
> cortex is worse than regular normalization.
>
> Since I am using mainly SPM5, I would like to know if I can safely use this
> FSL normalzation in SPM5 voxel wise analysis. Alternatively, can I run this
> kind of two-stage normalization in SPM5?
>
> Additional question is that if I can use this two-stage normalization,
> should I use the explicit mask (= the subcortical mask used in the second
> stage normalization of first_flirt) during the statistical analysis?
>
> Many thanks in advance.
>
> Buyean
>
>
>
>
>
>
>
>
>
>
>
>
>
> -----Original Message-----
>
> From: DRC SPM <[log in to unmask]>
>
> To: [log in to unmask]
>
> Sent: Thu, 25 Oct 2007 3:16 am
>
> Subject: Re: [FSL] sienax problem 512x512 scans
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi Buyean,
>
> > can one use SPM5 Display to reorient the image (Nifti) for FSL
>
> SPM5's reorientations get written to the NIfTI headers, so you could
>
> use FLIRT's -usesqform option to resample the reoriented images as
>
> Mark describes here:
>
>
>
> http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=fsl&P=40969
>
>
>
> However, I think Steve made the point that you should probably avoid
>
> the interpolation errors from such reorientation and resampling, by
>
> instead using only fslswapdim. As you said, it is limited to 90 degree
>
> rotations, but those have the benefit of being exact -- no
>
> interpolation is needed. Hopefully if you get the orientation correct
>
> to the nearest 90 degrees then the flirt calls within sienax should be
>
> successful. If not, you might be able to modify the sienax script to
>
> make use of the usesqform FLIRT option internally, but I haven't
>
> looked into that... (I hope this isn't the third idiotic email I've
>
> sent to this list recently... ;-))
>
>
>
> Note that manual reorientation is more important in SPM5 than in FSL,
>
> because at present the unified segmentation model in SPM5 doesn't
>
> model non-brain tissue very well, so its affine registration step
>
> needs a good rigid initialisation to succeed. (There are a few posts
>
> by John Ashburner on the SPM list with similar wording.) FLIRT on the
>
> other hand, uses a simpler, more general cost function, with a more
>
> sophisticated and robust optimisation routine (described in the tech
>
> reports, and the course slides last time I looked), which generally
>
> seems to be very good. In fact, I once played around with using FLIRT
>
> to generate the initial transformations for SPM5; this seemed to work
>
> well if the subjects can be successfully registered to MNI using rigid
>
> registration only, but gets complicated if you have to enable scaling
>
> for FLIRT to work well.
>
>
>
> Anyway, I'll stop waffling.
>
> Best,
>
> Ged
>
>
>
>
>
>
>
>
> ________________________________________________________________________
> Check Out the new free AIM(R) Mail -- Unlimited storage and
> industry-leading spam and email virus protection.

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

April 2024
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
2000
1999
1998


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