Discuss (controversial) issues


You can discuss R-fMRI related issues here, especially controversial issues. We invite all interested researchers to provide their opinions on the issues, as an immediate, efficient, direct and "peer-viewed" way to reach some level of consensus.

whole brain standardization or within a mask?

Submitted by MariaS on

Dear Experts,

for the analysis of our ALFF/fALFF and Reho values we use the z-maps within a graymatter mask. However the mask was only applied after calculation and standardization of those values for the group contrasts. Is this an unusual procedure? or should I use only the voxel within the mask for creating the z-maps?

Thanx in advance for feedback


rsfMRI Parkinson's Progressive Marker Initiative - Slice shifting

Submitted by LuisPerazaRo on

Dear Forum,

I downloaded the rsfMRI baseline from the Parkinson's Progressive Marker Initiave, but the odd thing is that all fMRIs look like the image below. There is a shift motion or slope every 8 slices but there is no information on internet about this kind of acquisition. Also articles using this database doesn't mention this characteristic in their Methods section. I wonder if somebody in this Forum has worked before with this database and faced this problem.

Many thanks, Luis R. Peraza

Regress out covariates

Submitted by nabila11 on

Hi experts, 

I'm quite new to REST for the  analysis of  my resting state data. I want to do functional connectivity analysis but i have problems when i want to regress out motion parameters and ROI signales from my data. 

I don't understand the way to arrange my covariates  (rp files and RoiSignals) in a specific folder ; so i can use them in the Regress Out Covariates step. Can you help me with that please ? 

Thank you, 

Best regards, 

Statistical Analysis

Submitted by ladansh on

Hi all.

I am quite new to REST and SPM, so my question might sound silly.

I want to do statistical analysis on ReHo and ALFF maps. I watched the DPARSF course videos and it says that in order to perform Statistical analyisis (One- Sample t Test), I have to calculate mReHo-1. 

correct me if I am wrong, It means that the null hypothesis would be : mReho-1 = 0. Which in turn means that I would be looking for voxels in which mReho is greater than one. 

I do not quite get the theory behind this... why not compare the results with 0 instead of 1? 

How to response the reviewer's comments about using degree centrality as the measure to identify hubs

Submitted by yaqiong on

Dear Chaogan,

I need some help from you to response the comments from the reviewer. In the analysis, I used degree centrality to measure the developmental changes in hubs with age, but the reviewer questioned it, and proposed questions like 'Why have the authors used only degree centrality as the measure to identify hubs ? Are the results robust against other graph centrality measures such as the  betweenness centrality ?'

Could you please give me some suggestion on how to response it? Thanks so much.



One sample t-test and significance

Submitted by David on


I have a group of 90 test subjects and I calculated FC for the left Amygdala. I used the DPABI statistical toolbox and calculated a one-sample t-test for the FC zmaps for the ROI with base 0. The results show very high t-values up to 40 in the seed region itself and up to 20 in other regions (see attached picture). I cannot correct for multiple comparison because any voxel with a t-value that high will be significant even when using FDR. I'm not sure if this is correct or if I did something wrong?

Any helpful comments appreciated

DMN: network differences between seed regions

Submitted by axel.vadim on



It is well-known that depending where we choose seed region of the DMN (e.g.., PCC or mPFC) we can get major difference between the networks. Why is that? If region A was correlated with region B, then it does not matter which of them was seed. Is it because the network we get is a statistical map? So, for example, the most strong correlation of A is with B. But B, has stronger connection with C. So, the when A is a seed I will see the B. But When B is the seed I will not see the A.