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: topup and eddy multishell different TE

From:

Jesper Andersson <[log in to unmask]>

Reply-To:

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

Date:

Fri, 7 Oct 2016 11:50:29 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (24 lines)

Hi again Pablo and Eduardo,

> 
> Assuming the B0 field doesn't change from acquisition to acquisition, what I would expect is that the B0 distortions do not depend on your TE, just on your EPI readout train (echo spacing, and number of EPI lobes).  Therefore, the distortions in the images collected with different TEs should be the same.  (You could test that by collecting data on a phantom --to make sure there is no motion-- with different TEs (and b-value=0, so there are no eddie current distortions), and see if the images themselves, not the topup estimates, are the same).
> 
> So, if topup gave different estimates of the field, it must be because the different intensities in the images (due to different TEs) confuses it, and it assumes there signal intensity increase/decrease comes from piling up/stretching the signal.  (Again, a way to test this would be to take your phantom data and scale all the images collected with different TEs so that all have the same intensity.  In that case, the distortions found by topup should be the same.  Then, you could applytopup to the un-scaled data).

estimating the B0 field from pairs of b0-volumes where different pairs have different echo time should give the same estimated field. The images are re-scaled internally to a grand mean of 100, so the intensity scaling should not matter. Things that matter are, for example, subject movement and shimming. If the subject moves between the acquisitions with different echo times that field will change. As a first approximation it will “move with the subject”, but in the case of rotations around an axis non-parallel to the magnetic flux is will undergo additional changes. If you get different fields from your b0:s without re-shimming and without subject movement, I cannot quite explain that. 

> 
> Now, for applying "eddy": in principle, the eddy currents would be different when you apply different diffusion-encoding gradients.  In the case of data collected with the same TE, normally the scanner would just apply stronger gradients to obtain higher b-values, but the timing would be the same.  Therefore, the eddy currents (and, hence, the distortions) would just scale up or down.  In the case of data collected with different TEs, supposing you selected the smallest TE possible for each b-value shell, the amplitude of the gradients would the the same (maximum), and the timing would be different.  If the principal component of the eddy currents decays fast, it could be that the short-TE and long-TE shells have identical eddy current distortions: those produced by turning off the diffusion-encoding gradient before the EPI readout).  So that might explain why eddy works fine with data collected with different TEs.  However, I would not assume this will be the case for every system (every scanner might have different eddy current characteristics).

As long as you don’t specify a 2nd level model in eddy (the --slm option, which is off by default) eddy makes no assumptions about how the eddy currents in one volume relates to the eddy currents in another. Therefore it doesn’t matter if the different shells have different echo times. If ones specifies for a example a linear 2nd level model (which one would have to do explicitly) eddy would assume that volume acquired with the same b-vec would have the same eddy currents (scaled by b-value) and then the echo time might potentially matter.

Jesper


> 
> Finally, as Jesper mentioned, combining diffusion data collected with different TEs is quite problematic, since the diffusion time will be different, and you will be probing the microstructure at different spatial scales.
> 
> Best,
> 
> -Pablo

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

April 2024
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