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  March 2009

SPM March 2009

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: SPM 5 / 8 NIfTI qForm and sForm Implementation

From:

John Ashburner <[log in to unmask]>

Reply-To:

John Ashburner <[log in to unmask]>

Date:

Fri, 13 Mar 2009 14:31:56 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (49 lines)

SPM counts its indices in the same way as MATLAB, starting at 1 (like an 
elevator does), whereas the actual encoding in NIfTI is in the C convention, 
starting and 0 (as you see in a British lift).  Unless I have made a mistake 
somewhere, this should be the same throughout SPM.

Apart from the imported images and flow fields generated by the DARTEL 
toolbox, SPM only uses one of the matrices. When images are created by SPM, 
both the sform and qform are set to encode the same transform (although some 
qform transforms can not be exactly represented, and a warning message will 
be generated).  Images are written with their qform_code and sform_code both 
set to 2.

When orientations are read, the sform is used in preference to the qform.  If 
the sform is not specified, then the qform is used.  If qform is not 
specified, then SPM assumes that images are stored axially and their 
left-right is determined by spm_flip_analyze_images.

Best regards,
-John

On Friday 13 March 2009 01:19, Bryce Wilkins wrote:
> Hi everyone,
>
> I have been evaluating SPM 5/8's compatibility with the NIfTI standard and
> am curious to know the extent that the different transformations qForm and
> sForm embedded in the NIfTI header (either .hdr or .nii file) are
> accommodated in SPM.
>
> When I display a NIfTI file that includes a header with only the *sForm*
> transformation, SPMs "Display" utility seems to display it correctly, and
> the origin reported is as expected, say at [128 104 30].  However, when I
> load the same image data with a header that includes only the *qForm*
> transformation, I find the origin (and thus voxel space/world space) is
> incorrect; e.g. the origin is now reported as [128 154 30].  It seems only
> the second co-ordinate is wrong.
>
> If I display my test data sets with MRIcroN or a NIfTI MATLAB toolbox, the
> origin is reported identical as expected in all cases.
>
> So, my question is, does SPM 5/8 only support one type of transformation,
> either sForm or qForm.  Which one should be used?
>
> Is the above inconsistency a bug that needs to be fixed?
>
> Thank-you for any comments to help me understand and resolve this problem!
>
> Regards,
> Bryce

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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