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Very clear. Thankyou so much. -Dianne On Wed, Apr 21, 2010 at 5:14 PM, Matt Glasser <[log in to unmask]> wrote: > 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]] *On > Behalf Of *Dianne Patterson > *Sent:* Wednesday, April 21, 2010 5:17 PM > *To:* [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] > University of Arizona > SLHS 328 > 621-5105 > > > > > -- > Dianne Patterson, Ph.D. > [log in to unmask] > University of Arizona > SLHS 328 > 621-5105 > -- Dianne Patterson, Ph.D. [log in to unmask] University of Arizona SLHS 328 621-5105