cat's blog

negative numbers for time courses

Dear R-fMRI Network team,
I am looking at the ROI Signals_ xxx which outputs the time courses for each ROI and I am surprised that some of these numbers are negative? Could you please explain why that would be the case?
With kind regards,
Catherine

reviewer questions

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". Was the filtering based on a 'discrete cosine transform' as done in SPM with the given frequencies used as cut-off, I believe this is correct, but just wanted to confirm.

motion regression

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

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?

ROI to ROI correlations

Dear Expert,

I successfully used DPARSF to define 33 ROI's and to extract the ROI time courses for my subjects.
I have two groups and I want to see if the connectivity within the 33 ROI differs between groups.

I would be grateful if you could advise me on how to set up this analysis in the dpabi "statistical analysis toolbox'. I am not sure what files I need to input from each individual. Are these the .mat files or the .txt files?

With kind regards,
Cat

ROI signal change

Dear Expert,

I have calculated the resting state BOLD signal for several ROI's using your valuable toolbox Dpabi in order to assess functional connectivity patterns between these ROI's.

I found out that the ROI_FCMaps for each person show my 120 time points (rows) for each ROI (columns).
I was surprised that some of the time point signal changes were up to negative 12 or positive 6, although most were somewhere between negative 4 and positive 4. Are these outliers? Should I be concerned about the validity of the time point data?

With Kind Regards,
Cat

ROI to ROI connectivity

Dear Experts,

I wish to examine the functional connectivity between 4 regions (ROI's) only. Is this a possibility in DPARSF A.
Or does DPARSF only measure the functional connectivity between the ROIs with the rest of the brain?
Very Kind Regards,
Cat

group analysis

Dear DPARSF A Experts:

Thank you for this valuable toolbox.
I have successfully pre-processed my data (20 healthy controls; 20 patients) using DPARSF A for a voxel-wise functional connectivity analysis with a pre-defined ROI. I had two resting state runs for each of my 40 subjects, so my data is organized as required by DPARSF into a folder named 'Analysis' under which I created two FunImg folders (FunImg, and S2_FunImg) for both resting-state runs. Therefore, I have now 2 Results folders that contain the zFCMaps for each person.

Bet error

Dear Expert:
I have 'sourced ' FSL in the terminal like this:
FSLDIR=/Applications/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
I then inputted the command 'bet' and received below options.

Usage: bet [options]

Then I opened matlab with the following command in the same terminal:
/Applications/MATLAB_R2012b.app/bin/matlab

Unfortunately, I am receiving another error message.
I would appreciate any help.
Very Best Regards,
Cat

Bet error: command not found

Dear Experts:

 I am new to DPARSF and new to Matlab,so please kindly excuse my basic question.

I am working on a Mac and have installed FSL and SPM8.  I have also opened Matlab from the terminal as suggested. I am able to start DPARSF (by adding path with subdirectories as suggested in Matlab) and it runs fine through the dicom-nifii conversion, the realign, estimate and reslice process until I receive the error message:

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