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  November 2011

SPM November 2011

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: 3d vs 4d realignment

From:

Joshua Balsters <[log in to unmask]>

Reply-To:

Joshua Balsters <[log in to unmask]>

Date:

Wed, 30 Nov 2011 14:50:01 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (170 lines)

Thanks John and Donald for taking the time to reply

Just to explain this thread fully for the archive I should add that
the differences in realignment parameters were NOT to do with 3D and
4D conversion but actually due to changing the image origin.



On 28 November 2011 13:12, John Ashburner <[log in to unmask]> wrote:
> The transformation parameters are expected to be different.  Here is a
> little snippet of code to illustrate the fact that the same
> transformation matrix (M) will give different voxel-to-voxel mappings
> when the data have different voxel-to-world mappings (R0 and R1)....
>
> R0=eye(4);
> R1=R0;
> R1(1,4)=20;
> M=spm_matrix(randn(1,6));
> R0\M*R0
> R1\M*R1
>
> Using motion parameters as regressors would give very slightly
> different results that are dependent on the reference space, but I
> don't think the effect is likely to be large.  The reason for the
> different results is that rigid-body motion is actually a nonlinear
> transformation (it can not be defined by a linear combination of
> spatial basis functions).  The matrix logarithm of a rigid-body
> transform can however be described by a combination of basis
> functions.
>
> M1 = [zeros(4,3) [1 0 0 0]'];
> M2 = [zeros(4,3) [0 1 0 0]'];
> M3 = [zeros(4,3) [0 0 1 0]'];
> M4 = [0 1 0 0;-1 0 0 0; 0 0 0 0; 0 0 0 0];
> M5 = [0 0 -1 0;0 0 0 0; 1 0 0 0; 0 0 0 0];
> M6 = [0 0 0 0;0 0 1 0; 0 -1 0 0; 0 0 0 0];
>
> p = randn(1,6);
> R = expm(p(1)*M1+p(2)*M2+p(3)*M3+p(4)*M4+p(5)*M5+p(6)*M6)
>
> The nonlinearities could be reduced by computing the transformations
> relative to some mean rigid-body transform.  If you are really
> interested, this (Karcher mean) could be computed as described in
> Roger Woods' 2003 paper "Characterizing volume and surface
> deformations in an atlas framework: theory, applications, and
> implementation".
>
> Best regards,
> -John
>
>
> On 25 November 2011 23:37, MCLAREN, Donald <[log in to unmask]> wrote:
>> John,
>> I was just looking into this and found the same thing. Different rp file
>> values with reoriented images.
>> hdr(1).private.mat
>>    -3.0000   -0.0000         0   97.5000
>>    -0.0000    3.0000    0.0000  -96.9129
>>     0.0000         0    4.5000  -56.4129
>>          0         0         0    1.0000
>>  hdr(1).private.mat0
>>    -3.0000         0         0   97.5000
>>          0    3.0000         0  -96.9129
>>          0         0    4.5000  -56.4129
>>          0         0         0    1.0000
>> and reoriented file:
>> hdr2(1).private.mat
>>    -3.0000   -0.0000    0.0000   97.5000
>>     0.0000    3.0000    0.0000  -56.9129
>>    -0.0000         0    4.5000  -86.4129
>>          0         0         0    1.0000
>> hdr2(1).private.mat0
>>    -3.0000         0         0   97.5000
>>          0    3.0000         0  -96.9129
>>          0         0    4.5000  -56.4129
>>          0         0         0    1.0000
>> It looks like the .mat fields are slightly different; however, the same for
>> all volumes. The question is thus, why are the realignment parameters
>> different if the same data is used, just different transformation matrices.
>> Additionally, since the rp files are different, using the motion regressors
>> as covariates would change the models as well.
>> Are the differences due to interpolation to produce the mean image resulting
>> in slightly different values?
>>
>> Best Regards, Donald McLaren
>> =================
>> D.G. McLaren, Ph.D.
>> Postdoctoral Research Fellow, GRECC, Bedford VA
>> Research Fellow, Department of Neurology, Massachusetts General Hospital and
>> Harvard Medical School
>> Office: (773) 406-2464
>> =====================
>> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
>> intended only for the use of the individual or entity named above. If the
>> reader of the e-mail is not the intended recipient or the employee or agent
>> responsible for delivering it to the intended recipient, you are hereby
>> notified that you are in possession of confidential and privileged
>> information. Any unauthorized use, disclosure, copying or the taking of any
>> action in reliance on the contents of this information is strictly
>> prohibited and may be unlawful. If you have received this e-mail
>> unintentionally, please immediately notify the sender via telephone at (773)
>> 406-2464 or email.
>>
>>
>>
>> On Fri, Nov 25, 2011 at 3:43 PM, John Ashburner <[log in to unmask]>
>> wrote:
>>>
>>> I don't have any ideas here.  I think you really need to take a close
>>> look at the data.  You can read the fields in the headers by:
>>>
>>>    P='blah.nii';
>>>    Nii=nifti(P)
>>>
>>> If you want to see the actual values, then you can look at a hidden
>>> field of the nifti object:
>>>
>>>    Nii.hdr
>>>
>>> Computing difference images via ImCalc, and displaying them via
>>> CheckReg can also help to give clues.
>>>
>>> Best regards,
>>> -John
>>>
>>> On 24 November 2011 10:53, Joshua Balsters <[log in to unmask]> wrote:
>>> > Dear SPMers
>>> >
>>> > I found one previous discussion on this point but not much else, so
>>> > apologies if I'm repeating what everyone already knows.
>>> >
>>> > I've recently starting using 4D files straight from the scanner (Philips
>>> > Acheiva) in SPM rather than splitting them into 3D files using fslsplit. I'm
>>> > finding in most cases there are subtle (+/-0.5mm) to drastic (over 2mm)
>>> > differences in my realignment parameters depending on whether I use the 4D
>>> > or 3D versions of the same datasets. These differences are only in the
>>> > translations and not the rotations.
>>> >
>>> > It would be great if anyone could explain why this happens. I had a
>>> > quick look for differences between the 3D and 4D files and I think the issue
>>> > is that fslplit is automatically changing my datatype from int16 to float32,
>>> > and i read in a previous discussion that it also changes the scaling factor
>>> > which is probably the bigger issue.
>>> >
>>> > any advice on this issue would be greatly appreciated!
>>> >
>>> > Best
>>> > Josh
>>> >
>>
>>



-- 
Joshua Henk Balsters, PhD
Visiting Research Fellow

Trinity College Institute of Neuroscience
Lloyd Building
Trinity College Dublin
Dublin 2
Ireland

Tel: +353 1 896 8405
http://people.tcd.ie/balsterj
http://tcd.academia.edu/JoshuaBalsters
http://www.tcd.ie/Neuroscience/niel/people/research-associates/j-balsters.php

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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

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