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  July 2008

SPM July 2008

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: SPM5 VBM DARTEL R/L question?

From:

John Ashburner <[log in to unmask]>

Reply-To:

John Ashburner <[log in to unmask]>

Date:

Fri, 4 Jul 2008 12:03:50 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (67 lines)

Maybe SPM should stop supporting ANALYZE 7.5 format, and use only NIfTI.  This 
would prevent any confusion about which are the left and right sides of the 
brain.

If you are using SPM5, then it does not flip the data during spatial 
normalisation.  This flag simply indicates that indexing of your data uses a 
left-handed system.  The stuff about radiological and neurological 
orientation is a bit of a distraction, as this only indicates the orientation 
of a single slice.  For example, you could rotate the volume by 180 degrees 
and have the left and right sides of the axial and coronal views reversed, 
but the handedness would remain unchanged (ie a rotation would not flip the 
images).

If you have certain types of DICOM files, then the DICOM import of SPM5 may be 
used to convert your data to NIFTI format.  If SPM5 can't deal with it, then 
here are a couple of sites that contain links to DICOM to NIfTI converters:

http://www.nitrc.org/
http://idoimaging.com/index.shtml

Providing you only use SPM5 or any other NIfTI compatible software, working 
with your data in this way should not lead to any ambiguity about left and 
right sides (unless there are bugs in the code that may cause the behaviour 
to be otherwise).  NIfTI files may end .nii, or they may be .img and .hdr, as 
in the old ANALYZE format.  If the files are NIfTI format, then the flip 
setting in spm_defaults.m is ignored, as this information is available in the 
headers.

However, if you use ANALYZE format images, then the flip setting may be used - 
depending on whether the images have a .mat file associated with them or not.  
If there is a .mat, then the flip setting in spm_defaults.m is ignored 
because the required information is in the .mat file.  If there is no .mat 
file for your ANALYZE format images, then the handedness needs to be 
determined from the spm_defaults.m file.

I WOULD SUGGEST THAT THE defaults.analyze.flip SHOULD NEVER BE CHANGED.  It is 
the responsibility of the user to ensure that the orientation of your images 
is as described http://www.fil.ion.ucl.ac.uk/spm/software/spm2/#Compatability 
prior to doing anything else in SPM2 or SPM5.  Provided this is satisfied, 
then the orientations should remain the same.  However, if you take images 
generated or modified using SPM5 (ie NIfTI format images), and try to do 
something with them in SPM2 (not NIfTI format), then the orientation flag in 
the NIfTI headers will be ignored, and the image orientations may become 
messed up again.

Best regards,
-John

On Thursday 03 July 2008 22:46, Manish Dalwani wrote:
> Hi SPM'ers,
>
> I checked the spm_defaults.m file in SPM5 and the defaults.analyze.flip = 1
> i.e. it flips during the normalization. I used the dartel tools to warp,
> segment and modulate the images into GM/WM.
>
> If my images were in radiological format (my anatomicals), would the
> results now be in neurological format because of flip being turned on? I
> had it turned off in SPM2 and wouldn't bother because I knew my final
> results matched my initial  input. I am just not sure how many times the
> images flip when it's turned on!
>
> Kindly advise!!!
>
> Manish Dalwani
> Sr. PRA
> University of Colorado at Denver

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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

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