REST-meta-MDD Consortium Data preprocessing parameters

Submitted by Valter Lundegårdh on

To whom it may concern, 

I recently got access to the wonderful Data consortium with MDD patients and Normal Controls which I have wanted to use for some of my work where I am mostly interested in the ROISignals. However, I have not been able to understand if the parameters used in REST, SMP8 and DPARSF are standarised, i.e. the same for every single hospital that has shared some of their final R-fMRI indices, or if the parameters are the same as the ones in the original papers published by the different research groups. 

Take for example the ROISignals data from indice 20 organised by Xin-Ran Wu. In their paper, source (30), they write that "... smoothing with a 6mm full-width at half-maximum Gaussian kernel." was done. Yet, in the data I downloaded from the FTP server the ROISignals file has the name ROISignals_FunImgARCWF, i.e there is no "S". According to this would be an indication that the data has not been smoothed.

My questions are thus: 

1. Are the parameters in REST, SMP8 and DPARSF (in particular for ROISignals) the same for every hospital or are they the same as the original study (for those studies that used ROISignals)?

2. If the parameters are the same for every hospital, where can I find all the parameter values? I.e. is there a place on this website which specifies which values a hospital should used in the pipeline when they want to create and share their R-fMRI indices. E.g. if they should use the EPI template in SPM8 for spatial normalisation and or which frequency the Band Pass filter should be set to. 

3. If the parameters are the same as the original study, is it then true, for the data organised by Xin-Ran Wu, that the ROISignals have been smoothed but that "S" in the folder name is missing for some other reason? If the data has not been smoothed, is there a way I can get access to the smoothed ROISignals data shared by the hospitals with their original parameter setting using this Consortium?

Thank you for reading this and I look forward to hearing from you soon. If anything is unclear in my post please do not hesitate to ask me about it. 

Kind regards, 

Valter Lundegårdh

YAN Chao-Gan

Mon, 03/22/2021 - 09:18

Hi Valter,

The data were re-processed for the REST-meta-MDD project, thus all the processing pipelines are the same to the PNAS paper (not same with each individual original study).
You can see the data structure here:
As there was no "S", that means the data were not smoothed before extracting ROI signals.