 |
 |
Thanks a lot! -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Stamatios Sotiropoulos Sent: Thursday, July 03, 2014 9:01 AM To: [log in to unmask] Subject: Re: [FSL] SNR An area outside the brain, with no visible artifacts present. Did you look at the paper I sent? They have some pretty clear examples there. Cheers Stam On 3 Jul 2014, at 13:50, Alshikho, Mohamad J. <[log in to unmask]> wrote: > Hi Stam, > Kindly, what do you mean by an area in the background?. Let's suppose that my ROI is the ACC and I will calculate the mean in this area. Where I should choose my second area to calculate the SD? > > Thanks, > Mohamad > From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of > Stamatios Sotiropoulos [[log in to unmask]] > Sent: Wednesday, July 02, 2014 5:15 AM > To: [log in to unmask] > Subject: Re: [FSL] SNR > > Hi Mohamad, > > It would make some sense to do that within regions that are expected to have constant intensity, the FA is not expected to be constant across WM. > > The easiest way to do an SNR calculation is choose a WM area on the > b=0 image and compute the mean intensity. Then identify a background > region outside the brain, that does not contain any artefacts (e.g > ringing), and compute the standard deviation (or the mean). Then you > can divide the two and you could use some correction factors to > account for the fact that the noise distribution is not Gaussian. See > for details the Appendix of > > http://www.ncbi.nlm.nih.gov/pubmed/17622966 > > A less biased way to obtain an SNR estimate when the noise is spatially variant (which is the case with the modern sequences) is to use two repeats of the same image (e.g. two b0s) and compute the mean of the sum and standard deviation of the difference within a ROI. > > Cheers > Stam > > > On 2 Jul 2014, at 03:45, M. alshikho <[log in to unmask]> wrote: > >> Hi FSL experts, >> In order to calculate the signal to noise ratio (SNR) in the right hemispheric white matter I did the following : >> 1. I used fslstats to calculate the mean and standard deviation (SD) >> for the right hemispheric white matter fractional anisotropy 2. I did >> calculate the SNR by dividing the mean and standard deviation >> SNR=mean/SD >> >> Kindly, Is this correct? >> Thanks for any suggestions or comments >> >> Mohamad > > > The information in this e-mail is intended only for the person to whom > it is addressed. If you believe this e-mail was sent to you in error > and the e-mail contains patient information, please contact the > Partners Compliance HelpLine at http://www.partners.org/complianceline > . If the e-mail was sent to you in error but does not contain patient > information, please contact the sender and properly dispose of the e-mail.