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  December 2010

FSL December 2010

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Help with Field Maps

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

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

Date:

Tue, 21 Dec 2010 01:22:07 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (49 lines)

Dear Paul,

I'm not quite sure why you are going to all this effort here.
Is the correction via the FEAT GUI working correctly or not?
If it is then you shouldn't need to do anything else except just
use the filtered_func_data output by FEAT in your resting-state
analysis.  Also note that the MELODIC GUI offers the same
options.

I really wouldn't ever expect people to be applying forward
warps themselves to any data.  This is done internally to get
a good alignment between the fieldmap and EPI data spaces,
although it is complicated by the fact that each has a 
distorted and undistorted space.

If there is some problem with the correction then please let
us know.  Otherwise, you shouldn't need to try and replicate
all the internal steps, and I would certainly never recommend
you inverting the forward warp, as these warps may not be
1-to-1 as the EPI distortion process in no way guarantees
that topology needs to be preserved (although in practice
it is never seen as this amount of warping is accompanied
by massive signal loss and so there is nothing left to see).

All the best,
	Mark




On 17 Dec 2010, at 17:27, Paul Guillod wrote:

> Hi there,
> 
> I am having trouble optimizing the field map corrections on my EPI resting-state data. I ran the pre-stats through feat which applied the B0 correction decently well, but I noticed when you forward warp the magnitude image in fugue to align with the base of the EPI series it is warped in the exact opposite direction than it should be (at least when you visually inspect FM_D_fmap_mag_brain_siglossed with EF_D_example_func in the feat output/warp directory - since my EPI set was phase encoded in the x-direction it is apparent on a coronal slice). Is this intentional for alignment purposes?
> 
> Normally when I forward warp the magnitude image for alignment with my EPI base I have to specify the opposite direction in fugue (x instead of x-) as when I save an undistorted output. That said, when I forward warp the magnitude image it aligns *incredibly* well with the distorted EPI. Since I already resampled the field map to the EPI grid, I was hoping to save the forward warp, invert it, and apply that to the EPI set (certainly potential for a novice error).
> 
> In the feat logs the shift map from fugue is saved as a warp to apply simultaneously with the rigid motion correction matrix using applywarp, so I figured that taking the forward shift, inverting it, and applying it to the EPI data would be more accurate than running the correction using a rigidly aligned undistorted field map to distorted data. However, my modest attempts have failed to achieve this. Even when I apply the inverted warp to the forward warped field map magnitude image (from fugue) it doesnt output the original magnitude image as one would expect (  f-1(f(x))=x assuming warp is 1-to-1 function, right?). So I checked the files where the shift map is converted to a warp and noticed a discrepancy between the output of the data corrected in fugue and the data corrected using the shiftmap *from* fugue.
> 
> For instance, in the main feat output directory the image example_func_orig_distorted is identical to warp/EF_D_example_func. The former is corrected using applywarp specifying the shift map from fugue for the output example_func whereas the latter is corrected using fugue directly to undistort the image into warp/EF_UD_example_func. Since the two are identical and corrected using the same shift map (one using fugue and the other using the converted warp map), the undistorted outputs should be identical as well, right? But when you compare the outputs they were shifted differently (warp/EF_UD_example_func was shifted more than example_func). Did I miss something or does fugue undistort data differently than applywarp? Or does the error lie in convert warp?
> 
> I apologize for the wordiness in the message, but would appreciate any assistance. No doubt I raised concerns that have formerly been addressed so please don't hesitate to redirect me. Still new to most of this stuff.
> 
> Thanks,
> 
> -paul
> 

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