[color=#000000]Dear Amir,[/color]
[color=#000000]That's an interesting question. There is no voxel-specific intensity normalization step that is typically applied to the functional data. There is a session-level scaling that is intended to re-scale the data to PSC units (this is controlled by the 'BOLD signal units' option in the [i]Setup.Options [/i]tab) but this is simply a global scaling factor (i.e. it applies the same scaling factor to all voxels) so it will not change those distributions. That said, as most functional connectivity measures are scale-invariant (e.g. the correlation between two voxel BOLD timeseries will be independent of the scale of these timeseries) pre-scan normalization or other intensity-normalization procedures will have no effect on those measures (there are a few exceptions to this, mainly the subject-specific singular value decomposition used potentially for denoising in voxel-to-voxel measures, or the principal component decomposition used within White and CSF ROIs also during denoising, which are not scale-invariant and would be affected by the choice of using pre-scan normalization and/or other manual intensity normalization steps, but I do not know of prior studies looking at the efficiency of these steps in the context of different intensity-normalization procedures)[/color]
[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by AmirHussein Abdolalizadeh:[/i][quote]Dear all,
After analyzing and visualizing the functional preprocessed data (montage; attached) of my subjects, I realized most subjects show dark-inside fMRI scans (hollow-resembling) while others do not. Checking their raw fMRI data showed that the "Prescan Normalization" was not active in their acquisition. I wonder whether there is any need for intensity normalization for the fMRI acquisitions, and whether it is done by "denoising" or not. I tried to do that on one of the subjects. Interestingly, before denoising there was a right-leaning skewness in the probability distribution which converts to a normal distribution after that.
Any help is appreciated.
Bests,
Amir[/quote]
[color=#000000]That's an interesting question. There is no voxel-specific intensity normalization step that is typically applied to the functional data. There is a session-level scaling that is intended to re-scale the data to PSC units (this is controlled by the 'BOLD signal units' option in the [i]Setup.Options [/i]tab) but this is simply a global scaling factor (i.e. it applies the same scaling factor to all voxels) so it will not change those distributions. That said, as most functional connectivity measures are scale-invariant (e.g. the correlation between two voxel BOLD timeseries will be independent of the scale of these timeseries) pre-scan normalization or other intensity-normalization procedures will have no effect on those measures (there are a few exceptions to this, mainly the subject-specific singular value decomposition used potentially for denoising in voxel-to-voxel measures, or the principal component decomposition used within White and CSF ROIs also during denoising, which are not scale-invariant and would be affected by the choice of using pre-scan normalization and/or other manual intensity normalization steps, but I do not know of prior studies looking at the efficiency of these steps in the context of different intensity-normalization procedures)[/color]
[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by AmirHussein Abdolalizadeh:[/i][quote]Dear all,
After analyzing and visualizing the functional preprocessed data (montage; attached) of my subjects, I realized most subjects show dark-inside fMRI scans (hollow-resembling) while others do not. Checking their raw fMRI data showed that the "Prescan Normalization" was not active in their acquisition. I wonder whether there is any need for intensity normalization for the fMRI acquisitions, and whether it is done by "denoising" or not. I tried to do that on one of the subjects. Interestingly, before denoising there was a right-leaning skewness in the probability distribution which converts to a normal distribution after that.
Any help is appreciated.
Bests,
Amir[/quote]