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  August 2013

FSL August 2013

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: eddy acquisition parameters

From:

"Harms, Michael" <[log in to unmask]>

Reply-To:

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

Date:

Wed, 7 Aug 2013 15:34:41 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (184 lines)

In my experience (as a Siemen's user, processing Philips data), "fat shift
direction = P" on a Philips machine is equivalent to "Phase enc. dir = P
>> A" on a Siemen's machine.  Regardless, the accuracy of the shift
>>direction is easy to test empirically by running the correction both
>>ways, and that is what I'd recommend others do as well.

cheers,
-MH

--
Michael Harms, Ph.D.

-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.           Tel: 314-747-6173
St. Louis, MO  63110                    Email: [log in to unmask]




On 8/7/13 10:24 AM, "Franz Liem" <[log in to unmask]> wrote:

>Dear Jesper and Alistair,
>
>Yesterday, I had a discussion with our MR-Physicist about this topic. I
>can say a little bit about the Phillip information. These are all
>slightly educated guesses, so it would be great if anybody could confirm
>that this information is correct.
>
>1. fold-over direction =  "AP"; only gives you the axis, not the
>direction (i.e. there is no PA option on the console).
>the direction can be found in fat shift direction =    "P"; (I guess this
>means A->P)
>
>2. wrt the readout time the following equation seems to give good results
>(see:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1008&L=FSL&D=0&1=FSL&9=A
>&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=62420 and
>http://www.spinozacentre.nl/wiki/index.php/NeuroWiki:Current_developments)
>
>"For Philips Acheiva, the best equation for echo spacing is
>echo spacing =(1000*wfs)/(434.215 *(etl+1))
>where wfs is the Philips value of water fat shift in pixels
>etl is the echo train length or Philips calls this the epi factor"
>you can obtain wfs and epi factor from your .par files (I am not sure if
>the values of the par files and the sequence are always equal, as
>angulation or other factors? might change wfs)
>
>Our MR-Physicist measured the echo spacing in the sequence. This
>measurement gave the same value.
>
>To calculate the total readout time for topup...: ES * (Epi factor - 1)
>
>
>Best,
>Franz
>
>
>Am 07.08.2013 um 16:57 schrieb Jesper Andersson:
>
>> Dear Alistair,
>>
>>
>> On 30 Jul 2013, at 02:25, Alistair Perry <[log in to unmask]>
>>wrote:
>>
>>> Thanks Jesper.
>>>
>>> Currently we have 2 studies, one is which is in the process of being
>>>collected on a Phillips 3T scannner. The other, is to be collected on a
>>>Seimens 3T Scanner. Thus, due to the release of the new eddy tool, we
>>>would like to optimally design our diffusion scans.
>>>
>>> I retrieved the exam card for both the Phillips and the Seimens (page
>>>6-9) studies, which I have attached and labelled study 1 and study 2
>>>respectively. I find that Phillips does not yield as much information
>>>as Seimens for researchers in terms of acquisition parameters (and
>>>perhaps the phase-encoding is set by default..). Can you find any
>>>indication on the exam cards regarding the phase-encoding direction for
>>>both scanners, and whether the diffusion directions are sampled on the
>>>whole sphere?
>>
>> For the Siemens file it is quite clear and the information you need is
>>
>> Phase enc. dir. A >> P
>> and
>> Echo spacing 0.73 ms
>>
>> The phillips file looks a little messier to my untrained eye. If I was
>>to guess something I would guess that
>>
>> fold-over direction =  "AP";
>>
>> implies A >> P
>>
>> and another guess is that
>>
>> WFS (pix) / BW (Hz) =  "14.681 / 29.6";
>>
>> tells you the BW in the PE direction. But I stress that those are only
>>guesses. I suggest you chat to your resident MR physicist about these
>>things.
>>
>>>
>>> Nevertheless, for our second study on the seimens 3T scanner.. At the
>>>moment, we are going to run with 72 directions (8 b0) at a b-value
>>>2700. Would you recommend that instead of using a blip up- blip down
>>>phase encoding, that we instead sample the diffusion directions on the
>>>whole sphere. And if so, how do we ensure this? I have read through the
>>>forums and through the literature that using blip up-blip down is only
>>>suitable for very long acquisition times.
>>
>> The directions in study2vectors are already on the whole sphere. The
>>best way to check this is to read the directions into an nx3 Matlab
>>matrix, plot that matrix using the Matlab command plot3 and then type
>>"rotate3D on" to allow interactive rotation of the resulting
>>point-cloud. I just did that to your directions and when rotating a
>>sphere shape emerges. If it had not been on the whole sphere I would
>>instead have seen a half-sphere (bowl) shape when rotating.
>>
>> I am not sure what you mean by "very long", bit you are probably right
>>that in your case (72 dir) you should not use blip-up-blip-down for all
>>your dwi images. Just make sure that you precede your dwi acquisition
>>with a couple of b=0 scans with reversed blips.
>>
>> Jesper
>>
>>
>>>
>>> Thanks,
>>>
>>> Alistair Perry
>>>
>>>
>>> On Tue, Jul 16, 2013 at 12:48 AM, Jesper Andersson
>>><[log in to unmask]> wrote:
>>> Dear Alistair,
>>>
>>> > I would like to try out the new EDDY tool, as our lab has high
>>>b-value data on a Phillips 3T scanner.
>>> >
>>> > However, in comparison to the traditional eddy_correct, I noticed
>>>that there are a few extra compulsory arguments that need to be defined.
>>> >
>>> > For starters, is there any possible way to check the direction of
>>>the phase-encoding and the total readout time, after the scans have
>>>already been collected.
>>> >
>>> > I have access to the exam card, but the only information I have been
>>>able to obtain is the phase-encoding direction for the y-axis (which is
>>>ant-post).
>>>
>>> are all scans collected with the same polarity (i.e. ant->post)? If
>>>so, it is important that the diffusion directions have been sampled on
>>>the whole sphere (N.B. that it is quite common that the directions are
>>>only sampled on the half sphere which give the same diffusion
>>>information but inferior information when it comes to corrections for
>>>eddy current distortions).
>>>
>>> You can calculate the total readout time as the dwell time multiplied
>>>by (n-1) where n is the number of echoes of your EPI acquisition. If
>>>you don't have that information you can put any value in there (e.g.
>>>0.1) which means that the fields you calculate will not be scaled
>>>correctly but the distortion correction ail still be the same.
>>>
>>> I quite think of eddy as a "prospective tool" in the sense that you
>>>may need to rethink your acquisition protocol (and what information you
>>>record in your scan log) slightly in order to get it to work optimally.
>>>
>>> Jesper
>>>
>>>
>>> >
>>> > Thanks
>>>
>>> <study2vectors.txt><study2examcard.pdf><study1examcard.txt>
>>


________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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