DPABI/DPARSF Stand-Alone Version For Record

Submitted by YAN Chao-Gan on

 

With DPABI V4.1, what you need to do is very simple:

1. With MATLAB.
1.1. Please go to http://www.rfmri.org/dpabi to download DPABI. 
1.2. Add with subfolders for DPABI in MATLAB's path setting.
1.3. Input 'dpabi' and then follow the instructions of the "Install" Button on DPABISurf.
2. Without MATLAB.
2.1. Install Docker.
2.2. Terminal: docker pull cgyan/dpabi
2.3. Terminal: docker run -d --rm -v /My/FreeSurferLicense/Path/license.txt:/opt/freesurfer/license.txt -v /My/Data/Path:/data -p 5925:5925 cgyan/dpabi x11vnc -forever -shared -usepw -create -rfbport 5925
/My/FreeSurferLicense/Path/license.txt: Where you stored the FreeSurferLicense got from https://surfer.nmr.mgh.harvard.edu/registration.html.
/My/Data/Path: This is where you stored your data. In Docker, the path is /data.
2.4. Open VNC Viewer, connect to localhost:5925, the password is 'dpabi'.
2.5. In the terminal within the VNC Viewer, input "bash", and then input:
/opt/DPABI/DPABI_StandAlone/run_DPABI_StandAlone.sh ${MCRPath}


Now please enjoy the StandAlone version of DPABISurf with GUI!


If you don't want to run with GUI, you can also call the compiled version of DPABISurf_run. E.g.,
docker run -it --rm -v /My/FreeSurferLicense/Path/license.txt:/opt/freesurfer/license.txt -v /My/Data/Path:/data cgyan/dpabi /bin/bash
/opt/DPABI/DPABI_StandAlone/run_DPABISurf_run_StandAlone.sh ${MCRPath} /data/DPABISurf_Cfg.mat

 
_______________________________________
Below is for older version of DPABI Stand-Alone.
The DPABI Stand-Alone Version was compiled based on MATALB 2016b, SPM12 (r6897), DPABI V2.3 and DPARSF V4.3. You can use DPABI without purchasing a MATLAB license. However, you have to sign the user agreement (contribute to the R-fMRI Maps Project) before using it.
 
1. Please install MATLAB Runtime R2016b (9.1) from http://www.mathworks.com/products/compiler/mcr/index.html. Or click here: Windows, Mac, Linux.
2. Please download DPABI Stand-Alone Version through: Windows, Mac, Linux.
Or use FTP software: Host: lab.rfmri.org Username: ftpdownload Password: FTPDownload Path: /sharing/DPABI/StandAlone/
Of note, you have to sign the user agreement  to get the unzip passcode.
3. Run DPABI:
1) In Windows, double click DPABI_StandAlone.exe
2) In Mac or Linux, run in terminal: ./run_DPABI_StandAlone.sh <mcr_directory>
<mcr_directory> is the directory where version 9.1 of the MATLAB Runtime is installed, e.g., /mathworks/home/application/v91
 
You can also use DPARSFA_run Stand-Alone Version to run the pipeline analysis using script without GUI. Please follow these steps.
1. Please install MATLAB Runtime R2016b (9.1) from http://www.mathworks.com/products/compiler/mcr/index.html. Or click here: Windows, Mac, Linux.
2. Please download DPARSFA_run Stand-Alone Version through: Windows, Mac, Linux.
Or use FTP software: Host: lab.rfmri.org Username: ftpdownload Password: FTPDownload Path: /sharing/DPABI/StandAlone/
Of note, you have to sign the user agreement  to get the unzip passcode.
3. Use DPARSFA_run to call the Setting file. You can use DPARSFA GUI to define the .mat setting file, or use any program which can write matlab .mat file (e.g., R), according to the instructions at http://wiki.rfmri.org/ConfigDPARSFA_run:
1) In Windows, run in command line: DPARSFA_run.exe D:\Data\DPARSFASetting.mat
2) In Mac or Linux, run in terminal: ./run_DPARSFA_run.sh <mcr_directory> /Data/DPARSFASetting.mat
<mcr_directory> is the directory where version 9.1 of the MATLAB Runtime is installed, e.g., /mathworks/home/application/v91
 
Here is an example: /DPARSFA_run_StandAlone_Linux/run_DPARSFA_run.sh /mathworks/home/application/v91 /DPARSFA_run_StandAlone_Linux/DPARSFA_run_mcr/home/yanlab/Soft/DPABI/DPABIV2.3StandAlone/DPABI/DPARSF/Jobmats/Template_V4_CalculateInMNISpace_Warp_DARTEL.mat /Data /Data/SubID.txt 0
 
With the support of DPABI/DPARSF, we sincere hope you can join the R-fMRI Maps Project (RMP) to assemble a big data collection of intrinsic brain activity maps for a variety of R-fMRI indices. Now we are forming a new RMP Consortium for Depression and Bipolar Disorders (RMP-CDBD). Please contact Dr. Chao-Gan Yan (yancg#psych.ac.cn) if you would like to join us in this exciting endeavor to improve the utility of R-fMRI for the diagnosis and treatment of depression and bipolar disorders!
 
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