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  October 2016

FSL October 2016

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Can eddy be used on our DTI data?

From:

"Buckless, Colleen" <[log in to unmask]>

Reply-To:

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

Date:

Mon, 10 Oct 2016 20:59:20 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (40 lines)

Hi Jasper,
We tried your suggestion of using the T2 instead of having a blip-up and blip-down b0. However, we have some concerns because the "eddy" data appears to be distorted. Given that we acquired our images using right to left encoding, our acqparams.txt had to be changed to reflect this. The fourth element  was also changed using the formula suggested on FSL website (the "dwell time" multiplied by "number of PE steps -1").
This is what our acqparams.txt file looks like.
-1 0 0 0.113
1 0 0 0.113
 Is this correct? Should the top row have a positive 1 because we don't have a blip up and down, but have a t2 instead? 
Thank you for all of your help,
Colleen

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Jesper Andersson
Sent: Friday, October 07, 2016 6:56 AM
To: [log in to unmask]
Subject: Re: [FSL] Can eddy be used on our DTI data?

Dear Colleen,

> I would like to know if it is possible to use "eddy" on our data. Our DTI images were acquired with single-shot EPI (SENSE factor 2.5) on a 3T 'Acheiva' scanner (Philips, Best, the Netherlands). Two runs were collected in each subject, with 32 gradient directions (b = 800 s/mm3) and one b0 in each run. Sixty 2.2-mm axial slices were acquired for each volume, with 0.9 mm in-plane reconstructed resolution. We also acquired a non-EPI axially acquired T2-weighted image. Is it possible to average the two runs together and then run eddy? Can we still use eddy even though we do not have opposite phase encoding directions?

yes, eddy does not require opposing PE directions. How well it works will depend a little on how your b-vecs are distributed. I know that some Phillips protocols have a rather funny distribution of b-vecs and I have seen problems with running eddy on such data sets.

You do need at least one pair of b0 volumes with opposing PE directions if you want to run topup in order to estimate the susceptibility induced off-resonance field. If you have that, you can then pass the topup output (field estimate) into eddy, which means that eddy will correct the data also for susceptibility distortions.

If you don't have that, you can still run eddy and correct your data for eddy currents and movement.

In your case, if the contrast in your T2-image is sufficiently similar to the b0-images, you may be able to use your T2 in lieu of a reversed-PE b0. In that case you stick one of your b0:s followed by the T2 image in a 4D file and make an acqparams.txt file looking something like

0 1 0 0.05
0 -1 0 0.00005

provided that the PE-direction in your EPI images is A<->P (if it is in the L<->R direction you put the 1 and -1 in the first column instead).

Jesper


> Thanks,
> Colleen
Disclaimer:
The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
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


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

For help and support help@jisc.ac.uk

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