Question about masks for nuisance regression of WM and CSF signal and SPM apriori masks

Submitted by David on
Forums
DPABI/DPABISurf/DPARSF

Hi,

I have a small ROI mask like BNST and want to subtract this mask from the white matter segmented files or the subjects before regressing WM signal. I used the normal segmentation procedure (not new segment) and get three different types of segmented WM and CSF -files (files starting with c2..., mc2..and wc2). I need to know which one is used for the nuisance regression in DPARSF when using Segment (instead of SPM apriori) in order to subtract my mask from those files beforehand.

关于预处理中的distortion correction

Submitted by liufeng on
Forums
我想用中文提问 (I want to post in Chinese)

各位老师好！

最近碰到了一个审稿问题如下：

The authors failed to do distortion correction in preprocessing. The inhomogeneous B0 field induced distortion usually happens at prefrontal lobe and cerebellar, where the current study mainly focus on. The absent of distortion correction may undermine the reliability of the results.

我想问下distortion correction应该如何做呢？什么软件可以做？

 

谢谢

reviewer questions

Submitted by cat on
Dear Sir, I am re-posting this question as I have not yet received an answer. We have several reviewer questions that I would kindly ask your assistance with and which relate to the use of your very valuable DPARSF toolbox. 1)Using DPARSF we have bandpass filtered at 0.01-0.1 Hz. The reviewer requested to precisely state the 'type of filter".

motion regression

Submitted by cat on
Dear Sir, In your DPARSF toolbox I selected "motion scrubbing" and selected the FD (power) option. The reviewer of our manuscript asked what the assumed head radius was? Would you be able to help with this? With kind regards, Catherine

band pass filter and degrees of freedom

Submitted by cat on
Dear Sir, We have several reviewer questions that I would kindly ask your assistance with and which relate to the use of your very valuable DPARSF toolbox. 1)Using DPARSF we have bandpass filtered at 0.01-0.1 Hz. The reviewer requested to precisely state the 'type of filter". Was the filtering based on a 'discrete cosine transform' as done in SPM with the given frequencies used as cut-off? 2) the other reviewer question was this: "How many degrees of freedom were left in the data after preprocessing"? I am a little lost with this question.

Nuisance Covariates Regression

Submitted by lihong001 on
Forums
DPABI/DPABISurf/DPARSF

Dear Chao-Gan,

 I am rerunning a dataset using a relatively older verions of DPABI _V1.2_141101 and spm8. Previously it worked well. This time the pipeline was broken several times. Now at the step of Nuisance Covariates Regression, it stopped again. For this step, for the option of Nuisance setting, I chose white matter, CSF, mask used Segment, method was CompCor with PC number of 5.  Here is the error message:

 Moving Coviables Removed Files: S0076 ok

??? Index exceed matrix dimensions. 

Error in ==> DPARSFA_run>(parfor_body) at 2674

output files

Submitted by chelsmar on
Forums
GraphVar

Hello again,

I have looked in the manual and tutorial but I can't find this information, I'm sorry if I've missed it.

Could you please explain the contents of the output files that I get when I choose calculate variables and export?  

Also, what are the contents of the files when I choose export from the results viewer?

If I wanted to do post-hoc analyses (for example, a correlation between degree and a clinical variable), which data from graphVar do I use for this.

Apologies for my ignorance, I am new to graph theory!  

Thanks in advance,

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