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  April 2010

FSL April 2010

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: AW: [FSL] What constitutes "noise" in diffusion images?

From:

Stamatios Sotiropoulos <[log in to unmask]>

Reply-To:

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

Date:

Thu, 22 Apr 2010 14:32:51 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (133 lines)

Hi,

the SNR in the B0 image will increase with the square root of the number of repeats. If you are after the effect on tensor-derived parameters, then that is not as straightforward. The optimal ratio NH/NL, with NH the number of images acquired at a high b-value and NL the number of B0 images, is given in (Jones, MRM, 1999 - See Fig 4) for tensor-derived parameters.

Hope this helps,
Stam


On 22 Apr 2010, at 12:29, Jiansong Xu wrote:

> How about the number of B0 images? Can more B0 images increase SNR?
> 
> Best Regards
> 
> Jiansong
> 
> The information contained in this message may be privileged and confidential. If you are NOT the intended recipient, please notify the sender immediately with a copy to [log in to unmask] and destroy this message. Please be aware that email communication can be intercepted in transmission or misdirected. Your use of email to communicate protected health information to us indicates that you acknowledge and accept the possible risks associated with such communication. Please consider communicating any sensitive information by telephone, fax or mail. If you do not wish to have your information sent by email, please contact the sender immediately.
> ===============
> Jiansong Xu, M.D., Ph.D.
> Dept. of Psychiatry
> Yale Medical School
> 2 Church St., Suite 215
> New Haven, CT 06519
> Tel: 203-785-5306
> Fax: 203-737-3591
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On Apr 22, 2010, at 12:58 AM, Andreas Bartsch wrote:
> 
>> Higher bandwidth (in Hz or Hz/pixel) reduces the ADC, i.e. the time spend in digitization, and therefore the SNR.
>> ________________________________
>> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Matt Glasser [[log in to unmask]]
>> Gesendet: Donnerstag, 22. April 2010 02:14
>> An: [log in to unmask]
>> Betreff: Re: [FSL] What constitutes "noise" in diffusion images?
>> 
>> Higher resolution leads to lower SNR (think of it as less amount of signal in each of smaller voxels, or a greater amount of signal in larger voxels).  Higher bandwidth refers to the value of the bandwidth number (which may be in Hz, I don’t remember), but it also does mean wider bandwidth per pixel.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> ________________________________
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Dianne Patterson
>> Sent: Wednesday, April 21, 2010 6:45 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] What constitutes "noise" in diffusion images?
>> 
>> Thanks so much!
>> 
>> So, for imaging resolution...is higher resolution better SNR (just takes longer to acquire)?
>> Is "higher" bandwidth equivalent to wider bandwidth?
>> 
>> Thanks a million,
>> 
>> Dianne
>> 
>> 1)       Subject motion (even after eddy current correction) is certainly highly correlated with poorer bedpostx reconstructions (fewer subsidiary fibers, more uncertainty in fiber orientations), so it would make sense that it would negatively influence FA estimates.
>> 2)       If the problem is severe you probably should exclude the subject.
>> 3)       SNR scales linearly with magnet strength, so you would expect lower SNR for a given number of DWIs acquired at 1.5T vs 3T, all other things being equal.
>> 4)       This is a more difficult question: parallel imaging itself tends to decrease SNR a bit; however, it also allows you to decrease the TE, which increases the SNR and reduces the distortions.  The same is true of partial fourier.
>> 5)       One tends to get worse SNR with higher bvalues, but better contrast to noise ratios (CNR).  For FA, I think it has been established that around b=1000 is optimal (SNR vs CNR), but much higher bvalues are optimal for estimating crossing fibers.  The exact optimum bvalue will also depend on your hardware, sequence, and imaging resolution, because all of these affect the SNR term.
>> 6)       Averaging multiple scans will increase SNR and reduce noise, so long as you properly corregister them and remove subject motion within the timeseries.
>> 7)       SNR varies with the number of DWIs acquired, so as long as you make up for fewer directions with more averages, the SNR should be the same.  That being said, your estimates of fiber orientations (and especially crossing fibers) will be worse with fewer directions, so it is always better to acquire more directions (unless you want two averages for something like phase up/phase down distortion correction).
>> 8)       I’m probably the least clear on what this does to SNR.  It is really bad for tractography because it allows for the creation of intermediate orientation fibers that can cause inaccuracies, but I don’t know how it affects the accuracy of FA values.
>> 
>> Other issues you have not considered:
>> 
>> 9)       SNR will vary depending on the coil you used (more channels are better), and the gradient set in the magnet (stronger gradients allow a lower TE and thus higher SNR).
>> 10)   SNR will vary depending on if you use a dual spin echo sequence vs a single spin echo, again because you can use a lower TE with a single spin echo (but eddy currents will be worse).
>> 11)   Imaging resolution has a big impact on SNR, of course.
>> 12)   Higher imaging bandwidth generally results in worse SNR but less distortions.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> ________________________________
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]<mailto:[log in to unmask]>] On Behalf Of Dianne Patterson
>> Sent: Wednesday, April 21, 2010 5:17 PM
>> To: [log in to unmask]<mailto:[log in to unmask]>
>> Subject: [FSL] What constitutes "noise" in diffusion images?
>> 
>> Dear Group,
>> 
>> Carlo Pierpaoli points out that noise in diffusion images can bias FA.  In fact, he suggests that FA may actually increase in the presence of noise.
>> I am trying to understand what factors might contribute to noise, and I would appreciate any feedback that could further my understanding:
>> 
>> Possible Sources of Noise:
>> 
>> 1) Movement of the subject (this seems like the most obvious)
>> 2) Problems with the scanner hardware (this one also seems obvious)
>> 
>> More tenuous:
>> 3) Lower Tesla strength? (e.g., 1.5T vs 3.0T)
>> 4) the use (or non-use) of parallel imaging (where parallel imaging results in less noise, right?)
>> 5) b-value choices for diffusion weighted images (smaller values...(e.g. 700) have less noise than larger values (e.g. 1500)...?
>> 6) Averaging multiple runs (should reduce noise, right?)
>> 
>> Really tenuous:
>> 7) Fewer directions??? 6 vs 30 directions...is there more "noise" when you gather only 6 directions, all else being equal?
>> 8) upscanning the voxels (e.g, 96x96 matrix saved out as 256x256)...does upscanning contribute to noise?
>> 
>> Thanks in advance for your insights,
>> 
>> -Dianne
>> 
>> 
>> --
>> Dianne Patterson, Ph.D.
>> [log in to unmask]<mailto:[log in to unmask]>
>> University of Arizona
>> SLHS 328
>> 621-5105
>> 
>> 
>> 
>> --
>> Dianne Patterson, Ph.D.
>> [log in to unmask]<mailto:[log in to unmask]>
>> University of Arizona
>> SLHS 328
>> 621-5105
> 

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