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  September 2014

FSL September 2014

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: FUGUE echo spacing calculation

From:

Ajay Kurani <[log in to unmask]>

Reply-To:

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

Date:

Thu, 18 Sep 2014 18:46:55 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (28 lines)

Hi Mark,
   After more reading (particularly http://www.nitrc.org/forum/forum.php?thread_id=3785&forum_id=1456) I think I have a few questions regarding the optimal pipeline to incorporate FUGUE/epi_reg along with slice timing, physio and volume motion correction for resting state data.  

A) Having a siemens interleaved EPI sequence with physio collected I want to create a pipeline to incorporate physio correction, slice time , motion as well as Fugue for resting state data.  FUGUE is used to correct for B0 inhomogeneity.  The question I have is since the head moves a bit from volume 1 to volume 280 do I still run fugue first or do I need to run some sort of motion correction prior to that fugue applies the distortion correction to the appropriate voxels (ie in case of shift)?  On one hand the map is collected prior to the first volume so should I motion correct all EPI volumes to the first timepoint or can I use the last (my ref frame for motion correction) in order to ensure the map matches the brain position.  On the other hand the brains were in reality shifted when the EPI was taken so would the field map correction be incorrect since we adjust the position through volume correction, which does not represent the voxels true position in the magnetic field when the scan was acquired (ie run FUGUE PRIOR to motion correction).  My guess is that we should motion correct first and then run FUGUE and I can align to the last time point, but please confirm.


B) Aside from just motion correction I am trying to have the optimal pipeline to incorporate fugue with standard slice timing, motion correction etc.
The following passage is from the link I attached above:

"slice timing correction will make physiologic noise in your data unrecoverable by any means.  The slice time correction resamples the data acquired at X msec after the start of the volume and assumes that everything is Nyquist-sampled (ie. no freq higher than 1/(2*TR) Hz).  Any frequency lower than the Nyquist is correctly resampled as if it occurred at the start of the volume.  However, any frequency in the data that is higher than the Nyquist gets smeared all over the Fourier spectrum randomly depending on where it happened to bin.  Most (possibly anything slower than 200-400msec TR, due to higher harmonics of cardiac) acquisitions do not have a volumetric sample rate fast enough to capture physiologic noise."  

For some earlier datasets we do not have physio so I was going to use seed-based regression of CSF/Saggital sinus which captures physio signal and use as a regressor.  Based on the above does this mean that I would not be able to use this method due to the fact that slice-timing was performed?  Or would this still be a valid approach?

C) For data that I do have physio collected for, does the order below make sense to incorporate fugue, or any modifications you suggest? :

1) Run some sort of physio correction using physio data 
2) Run slice time correction
3) Discard initial timepoints since  steady state was not reached yet.
4) Run motion correction to the last time point (since first few time points will be discarded we align to last timepoint)
5) Align the magnitude/fieldmap image to the last time point  and apply then apply FUGUE



Sorry for the long email!!!!

Thanks,
Ajay

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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

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