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.

The issue with ALFF, fALFF, ReHo and FC results

Submitted by ygwang on

Dear R-fMRI, 

1. I did pre-processing and got the ALFF, fALFF, ReHo results by DPARSF, and then I used zALFF, zfALFF, zReHo files for the 2 sample t-test which I did in the SPM12. But there are some activation regions outside the brain, and the results look very strange. What should I do? Do these results convincing? 

How to use the first eigenvariate to calculate in the functional connectivity of resting state fMRI.

Submitted by 沈阳 on
When we used the seed-based ROI to calculate functional connectivity, the methods is “A seed reference time course was obtained within each ROI. Correlation analyses were conducted on the seed reference and the whole brain in a voxelwise manner for each ROI”. Recently, our article which used this methods was advised by the reviewers to use the first eigenvariate instead of a seed reference time course.

How to deal with behavioral variables correlated with mean framewise displacement (FD)?

Submitted by guiziwu on

Dear all,

As the requirment for resting-state fMRI studies on controlling head motion is becoming stricter and stricter. Typically we have to use a more stringent criteria to exclude participants for the head motion. For example, conducting scrubbing in the preprocessing and excluding participants who have large mean framewise displacement (FD) (e.g., FD > 0.2, 0.15). And we also need to make sure that our behavioral variables are not correlated with the mean FD, to convice the reviwers that our results are not influenced by the head motion.

About Power_Neuron_264ROIs_Radius5_Mask

Submitted by Spiral on

Dear all,

        Recently, I calculated the  large-scale FC by used Power's mask. But after that, I suddenly found out that the node of this mask does not have a specific name to indicate which brain area it belongs.

So, for now, I am really confused, and cannot found the details about the node of mask.

        Looking forward all fellow's help!




Gissian random field for multiple correction

Submitted by JiangYuchao on

Dear experts,

I used Gissian random field (GRF) in DPABI  for multiple correction when comparing rs FC maps differences between patient groups.

However, a reviewer suggested "this method (GRF) is based upon the hypothesis that the spatial smoothness of BOLD signal in the whole brain is consistent and the distribution of the spatial autocorrelation function in accordance with specific curve. Practically, the BOLD data is hardly accord with the hypothesis".

Paired T-test in RS comparison

Submitted by Liz on

Dear Experts,

I am new to FSL and RS signal analysis, so I need a help to understand the methods and the results of a preliminary fcMRI study that my supervisor has been working through.

He wanted to test variation in connectivity within motor circuits at rest. It is a single group design with repeated measures, divided into three parts: baseline RS scan, task performance and control RS scan. The idea was to compare the two RS scans in order to see variation in connectivity after the task performance, thus expecting increase functional connectivity within motor circuits.


Submitted by yubing on



审稿人除了指出样本和效应量的问题以外,还提出“Is there a bias for picking up ROI seeds correlated with GENE and then evaluating the relationship between GENE with the FC connected to these seed ROIs?'