Hi,
Stam answered this in his reply. I recommend that you follow his advice on this.
All the best,
Mark
On 2 Jul 2014, at 13:18, "Alshikho, Mohamad J." <[log in to unmask]> wrote:
> Hi Mark,
> 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? Can I use the CSF or the ventricles ?
>
> Thanks,
> Mohamad
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
> Sent: Wednesday, July 02, 2014 2:47 AM
> To: [log in to unmask]
> Subject: Re: [FSL] SNR
>
> Hi,
>
> The formula for SNR is fine here, but the trick is where you calculate the mean and SD from. If you want a good estimate of the background noise then you should measure the SD from an area in the background of the image, where there is no anatomical signal (and associated true anatomical variation) and also where there is no artefact (check that it is not an area with ghosting or other artefacts). The mean signal should be calculated from the area of interest, but make it as uniform as possible, particularly avoiding having multiple tissue-types, or anything with significantly different intensity, within the ROI that you use for this calculation.
>
> All the best,
> Mark
>
>
> 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
>
>
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