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

Help for FSL Archives


FSL Archives

FSL Archives


FSL@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

FSL Home

FSL Home

FSL  April 2010

FSL April 2010

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: AW: [FSL] EPI distortion of DTI

From:

Matt Glasser <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 19 Apr 2010 14:04:52 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (88 lines)

Hi Andreas,

I have used this on a few datasets, and was satisfied that the correction
produced fewer problems than the original distortion.  That being said,
FNIRT will make small changes in dimensions other than the phase encoding
direction of the diffusion images (where there isn't any EPI distortion and
the registration should be satisfied with translations and rotations)
because the FA and T1 do not have the same contrast in all tissues, and
there isn't a good way of restricting this.

Peace,

Matt.

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Andreas Bartsch
Sent: Monday, April 19, 2010 1:40 PM
To: [log in to unmask]
Subject: [FSL] AW: [FSL] EPI distortion of DTI

Quite clever! Have you tried - were you satisfied?
Cheers-
Andreas

________________________________________
Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Matt
Glasser [[log in to unmask]]
Gesendet: Montag, 19. April 2010 19:45
An: [log in to unmask]
Betreff: Re: [FSL] EPI distortion of DTI

You can use FNIRT to register the FA to the T1 and then apply the warpfield
generated to unwarp the raw data:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;XnD16g;20080923081452%2B0
100

To do this right, you may want to register your FA to T1 with FLIRT (I would
use 6 dof for this), then register the output FA to the T1 with FNIRT,
invert the FLIRT transform and then transform the warpfield into the
original diffusion space using the inverted FLIRT transform, so that you can
avoid needing to rotate your gradient table, and then unwarp the raw data.
Alternatively, you will need to apply the rotational components of the
original FLIRT linear transform to your bvecs file which can be found using
avscale --allparams and there is a rotate_bvecs script that you can use to
do the rotation.

This process is fairly complex, and definitely not ideal.  It is much better
to acquire field maps or correct for distortion by acquiring phase up and
phase down averages.  A lot of papers do not correct for EPI distortion, so
one can also choose not to do this.  If you don't correct for it, though,
you cannot rely on good alignment between your diffusion and structural data
in particular brain regions, like the temporal lobe and the orbitofrontal
region.  Depending on what you are trying to do with the data, this can be a
problem or not.

Peace,

Matt.

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Eunjin Yoon
Sent: Monday, April 19, 2010 3:49 AM
To: [log in to unmask]
Subject: [FSL] EPI distortion of DTI

Hello, all

I'm beginner of FSL and DTI processing.
I am really wondering how to process distorted diffusion tensor images.

My images from 3T phillips scanner show some distortion in frontal area.
I want to correct this distortion, but I don't have filed maps.
And most of papers using DTI, they didn't mention about how they dealt with
this type of problem.

First of my problem during DTI processing is making brain mask using BET.
Is it necessary that all of the distorted part is included as brain?
If some part of the distorted areas cut off from the brain, is that problem
for following process or if all of the distorted areas are included as
brain, will it make a problem?
OR Should I correct the distortion?
If I should do that, how to do that when I don't have field maps?

Thanks in advance.

EJ

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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


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