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...vation as the signal of interest. With regard to the first set, these formulae can be interpreted as definitions of effect size based on means or differences between means, like for example Cohen’s d =-=[45]-=-. As such it is a direct indication of the strength of the signal. Note that in our literature search, we also found possible negative SNR values, which might be confusing to many neuroscientists. The...

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...initions, we applied the SNR/CNR definitions in the context of experimental fMRI data and resting-state fMRI data. The experimental fMRI dataset is based on a houses-faces object recognition paradigm =-=[14]-=- and is freely available through the OpenfMRI project (http://openfmri. org). Forty 3.5-mm-thick sagittal images were acquired on a GE 3T scanner (General Electric, Milwaukee, WI) with TR = 2500 ms, F...

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... 4 (CNR). Another possibility is to model the strength of the signal based on the standard deviation of the activation signal [29–35], sS sN : This definition is also implemented in the DCM simulator =-=[36]-=- and is a very intuitive measurement of CNR because the ratio of the fluctuations of both activation signal and noise is calculated. Definition 5 (CNR). [37] and [38] used the ratio of the variances, ...

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...ged (i.e. a region from which no tissue signal is obtained) or the standard deviation from the noise distribution when known (e.g. the background noise in magnitude data follows a Rician distribution =-=[3]-=-). By varying, for example, field of view, scan parameters, magnetic field strength and slice thickness, the SNR of MRI images can be increased because these parameters influence the background noise....

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...a PLOS ONE | www.plosone.org 3 November 2013 | Volume 8 | Issue 11 | e77089 Definition 2 (CNR). In contrast, an amplitude measurement can be related to the standard deviation of the noise [21–24] and =-=[25]-=-, A sN : The amplitude of the signal is generally defined as the absolute difference between the baseline of the signal and the signal peak (Figure 2). Definition 3 (CNR). The previous definition of t...

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...4 cm, TE = 30 ms and flip angle = 90. This resulted in 1452 volume scans. For the resting state data, we randomly selected one subject (AnnArbor-sub04111) from the 1000 Functional Connectomes project =-=[15]-=-. These data, consisting of 295 resting scans, were acquired at 3T field strength with a voxel size of 3:75|3:73|3, a matrix of 64|64 and TR of 2s. Results Reported SNR values in the literature Report...

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...y of them are in fact CNR measurements. Definition 1 (SNR). The first definition models SNR based on the mean signal of the fMRI time series and the standard deviation of the noise in the time series =-=[19,20]-=-, S sN : As such, the global signal level, comprised of the baseline and activation, is related to the noise. Figure 3. Percentage of the 119 simulation studies from the literature search that report...

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... comparison between imaging hardware, imaging protocols and acquisition sequences. In this context, SNR is conceptualised by comparing the signal of the MRI image to the background noise of the image =-=[1,2]-=-. Mathematically, the SNR is the quotient of the (mean) signal intensity measured in a region of interest (ROI) and the standard deviation of the signal intensity in a region outside the anatomy of th...

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...bject (i.e. cardiac and respiratory pulsations, motion) and the task that is performed. Using time series outside the brain as noise measurement only, will not be sufficient to capture the noise data =-=[1,7,8]-=-. Secondly, since the main goal of fMRI studies is to detect small fluctuations over a period of time, image SNR might not be suitable. Therefore, temporal SNR (tSNR), in which the (mean) signal over ...

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...ll in terms of its relationship with the MRI acquisition parameters. Several studies have demonstrated the dependence on these parameters and illustrated the necessary conditions to obtain higher SNR =-=[1,7,10]-=-. Also the relationship between SNR and CNR (contrast-to-noise ratio, a measure of image quality based on a contrast rather than the raw signal) has been investigated. For example, Wald investigated t...

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...ver a period of time, image SNR might not be suitable. Therefore, temporal SNR (tSNR), in which the (mean) signal over time is taken into account, can be used to determine the SNR of fMRI time series =-=[9]-=-. How to define SNR for MRI and fMRI data is documented quite well in terms of its relationship with the MRI acquisition parameters. Several studies have demonstrated the dependence on these parameter...

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...bject (i.e. cardiac and respiratory pulsations, motion) and the task that is performed. Using time series outside the brain as noise measurement only, will not be sufficient to capture the noise data =-=[1,7,8]-=-. Secondly, since the main goal of fMRI studies is to detect small fluctuations over a period of time, image SNR might not be suitable. Therefore, temporal SNR (tSNR), in which the (mean) signal over ...

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...y of them are in fact CNR measurements. Definition 1 (SNR). The first definition models SNR based on the mean signal of the fMRI time series and the standard deviation of the noise in the time series =-=[19,20]-=-, S sN : As such, the global signal level, comprised of the baseline and activation, is related to the noise. Figure 3. Percentage of the 119 simulation studies from the literature search that report...

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...a review). Translating SNR of MRI images to fMRI images is not as straightforward as it may seem. First of all, the noise in fMRI images does not correspond to the background noise of MRI images (see =-=[6]-=- for an excellent overview). In fMRI images, system noise effects the image as well as noise stemming from the subject (i.e. cardiac and respiratory pulsations, motion) and the task that is performed....

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...rameters influence the background noise. On the other hand, scanning hardware has also a major influence on the SNR levels of fMRI data. For example, SNR increases almost linearly with field strength =-=[4]-=- and is largely effected by the receiver coils (see [5] for a review). Translating SNR of MRI images to fMRI images is not as straightforward as it may seem. First of all, the noise in fMRI images doe...

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...and, scanning hardware has also a major influence on the SNR levels of fMRI data. For example, SNR increases almost linearly with field strength [4] and is largely effected by the receiver coils (see =-=[5]-=- for a review). Translating SNR of MRI images to fMRI images is not as straightforward as it may seem. First of all, the noise in fMRI images does not correspond to the background noise of MRI images ...

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...t-to-noise ratio, a measure of image quality based on a contrast rather than the raw signal) has been investigated. For example, Wald investigated the improvement of BOLD CNR at higher field strength =-=[11]-=-. He showed that BOLD CNR is not directly affected by most acquisition parameters such as reciever coil choice, parallel imaging acceleration and voxel size, but only through the influence on the tSNR...

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...sted. The obtained power is defined as the average number of correct detections (i.e. rejection of null hypothesis) over all time series. All simulations were carried out using the R package neuRosim =-=[13]-=-. Data acquisition As an illustration of the discussed definitions, we applied the SNR/CNR definitions in the context of experimental fMRI data and resting-state fMRI data. The experimental fMRI datas...

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...d caused by a combination of bias and voxel size [16]. An interesting observation was that Hughes and Beer made an explicit distinction between SNR for active clusters and SNR for non-active clusters =-=[17]-=-. In the simulation studies, the reported values varied widely across studies and were almost exclusively labelled as SNR. For example, the SNR for the simulations varied from 1 to 10 in one study, wh...

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...sed on a static image or time series. So for fMRI data, using the CNR of the time series instead of (t)SNR is more preferred because CNR compares a measure of the activation fluctuations to the noise =-=[12]-=-. In short, image SNR should be used to assess data quality of a single image, while tSNR gives information on the data quality of fMRI time series. CNR on the other hand, provides knowledge on how ea...

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...t one study reported the possibility of a CNR value as low as 0.01, but this was specific to the imaging of orientation columns in the visual cortex and caused by a combination of bias and voxel size =-=[16]-=-. An interesting observation was that Hughes and Beer made an explicit distinction between SNR for active clusters and SNR for non-active clusters [17]. In the simulation studies, the reported values ...

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... and the possible fluctuations in the signal due to the experimental task. In general, S can be calculated as the average haemodynamic response function (HRF) of the fMRI time series in a certain ROI =-=[18]-=-. The noise signal, N , will typically be the composition of several noise sources such as system noise, physiological noise and task-related noise. When referring to the noise signal, we implicitly t...

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...n is also implemented in the DCM simulator [36] and is a very intuitive measurement of CNR because the ratio of the fluctuations of both activation signal and noise is calculated. Definition 5 (CNR). =-=[37]-=- and [38] used the ratio of the variances, s2S s2N , which is of course equal to the square of Definition 4. Definition 6 (CNR). Again, the ratio of the standard deviations is also found in dB scale [...

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... implemented in the DCM simulator [36] and is a very intuitive measurement of CNR because the ratio of the fluctuations of both activation signal and noise is calculated. Definition 5 (CNR). [37] and =-=[38]-=- used the ratio of the variances, s2S s2N , which is of course equal to the square of Definition 4. Definition 6 (CNR). Again, the ratio of the standard deviations is also found in dB scale [39–44], 1...