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 2008

SPM October 2008

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: FSL 2 SPM

From:

Kathy Pearson <[log in to unmask]>

Reply-To:

Kathy Pearson <[log in to unmask]>

Date:

Wed, 8 Oct 2008 09:55:01 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (170 lines)

Pia,

FSL has utilities called "avwhd" (FSL 3.3 or before) and "fslhd" (FSL after
3.3) that may be helpful to you in determining exactly what is in an Analyze
or NIFTI header generated by any software.  How the files are viewed in SPM
and FSL is a separate question though.  Sometimes the qform information in
the file header may be different between FSL and SPM.  In addition to
avwhd/fslhd, FSL has numerous other "avw" and "fsl" command-line routines
that can be useful in reading or modifying file headers.

Kathy Pearson
UAB Psychology

-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On
Behalf Of Pia Rotshtein
Sent: Tuesday, October 07, 2008 1:04 PM
To: [log in to unmask]
Subject: Re: [SPM] FSL 2 SPM

Hi John,
Thanks for the replay.
The thing is that we have being using SPM for co-registration and
nevertheless we get that off-set, which is not viewed when presenting
with FSL (even tough the images are co-registered in SPM).
Which made us think that there is something hidden in the *.hdr, that
when presenting with SPM shift the image, or vice versa.
Given that these images have been processed by FSL first (to generate
the FA maps of DTI), we thought it is something that FSL add to the
header. We just not sure where this thing maybe hidden.
I guess I should ask the FSL people ;o).

Does that make any sense?

Thanks

Pia


-----Original Message-----
From: John Ashburner [mailto:[log in to unmask]] 
Sent: 07 October 2008 18:48
To: Pia Rotshtein; [log in to unmask]
Subject: Re: [SPM] FSL 2 SPM

Hi Pia,
I'm not too sure of the details of how FSLview displays images, but in 
general, the coregistration in SPM is more robust if given reasonably
good 
initial starting estimates.  Sometimes though, even this does not help -

particularly if the anatomical images were collected at high field and 
contain large intensity inhomogeneities.  One thing that you could try
is to 
segment the anatomical image first, so that a bias corrected version is 
generated.  Coregistration can then be done with the bias corrected
version.  
Note that if you do this, the coregistration should have the bias
corrected 
anatomical as the target and the FA image as the source (with any other 
images that are in alignment with the FA specified as "other").  This
should 
allow the original *_seg_sn.mat to be used for spatially normalising the
FA.

All the best,
-John

On Tuesday 07 October 2008 10:04, Pia Rotshtein wrote:
> Hi Tom,
>
> Thanks for the reply,
>
> We exhausted few options, converting to *.nii, *.img, *.hdr
>
> It just seem like the origin register by SPM are different
(spm_vol.m).
>
> We figure there is something else hidden in the hdr, that FSL reads
and
> write but SPM do not but could not find what.
>
>
>
> Will look at the discussion in the FSL list
>
>
>
> Cheers
>
>
>
> Pia
>
>
>
>
>
>
>
> ________________________________
>
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
> On Behalf Of Thomas Nichols
> Sent: 06 October 2008 22:43
> To:
> Subject: Re: [SPM] FSL 2 SPM
>
>
>
> Hi Pia,
>
> Have you double-checked that all of the images are true NifTI images
> (and not Analyze)?  (fslinfo will tell you).  If you've got a mix of
> Analyze and NifTI you'll have trouble.
>
> OTW, you're might be having qform-sform nightmares.  See a thread on
the
> FSL list "MNI Space in MRIcro and FSL" from 2007.
>
> -Tom
>
> On Mon, Oct 6, 2008 at 7:22 PM, Pia Rotshtein <[log in to unmask]>
> wrote:
>
> Hi everyone,
>
> Our aim is to co-register FA maps to T1 images.
>
>
>
> We have tried with both SPM and FSL.
>
> FSL seem to be doing a good job, and when check with FSLview it is
> perfect, but when checked with SPM5 check-reg it seems to be offset
> (mostly on the y,z dimensions).
>
> Similarly, when SPM is co-registering, when we check with FSLview it
is
> perfect, but with SPM check-reg it is offset (mostly on the y,z
> dimensions).
>
>
>
> We have read that the scales are different in FSL-nifti and SPM-nifti
> but we could not understand how to go about it.
>
> We want to end up with both images co-registered in SPM so we could
> apply the normalization parameters of the T1 to the FA images.
>
>
>
> Any advice would be appreciated
>
>
>
> Thanks
>
>
>
> Pia (& Magda)
>
> ____________________________________________
> Thomas Nichols, PhD
> Director, Modelling & Genetics
> GlaxoSmithKline Clinical Imaging Centre
>
> Senior Research Fellow
> Oxford University FMRIB Centre

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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