DPABISurf V1.1 Is Released

Dear Colleagues, 

We are pleased to announce the release of DPABISurf V1.1!

DPABISurf is a surface-based resting-state fMRI data analysis toolbox evolved from DPABI/DPARSF, as easy-to-use as DPABI/DPARSF. DPABISurf is based on fMRIPprep 1.4.1 (Esteban et al., 2018)(RRID:SCR_016216), and based on FreeSurfer 6.0.1 (Dale et al., 1999)(RRID:SCR_001847), ANTs 2.2.0 (Avants et al., 2008)(RRID:SCR_004757), FSL 5.0.9 (Jenkinson et al., 2002)(RRID:SCR_002823), AFNI 20160207 (Cox, 1996)(RRID:SCR_005927), SPM12 (Ashburner, 2012)(RRID:SCR_007037), PALM alpha112 (Winkler et al., 2016), GNU Parallel (Tange, 2011), MATLAB (The MathWorks Inc., Natick, MA, US) (RRID:SCR_001622), Docker (https://docker.com) (RRID:SCR_016445), and DPABI V4.1 (Yan et al., 2016)(RRID:SCR_010501). DPABISurf provides user-friendly graphical user interface (GUI) for pipeline surface-based preprocessing, statistical analyses and results viewing, while requires no programming/scripting skills from the users.

The DPABISurf pipeline first converts the user specified data into BIDS format (Gorgolewski et al., 2016), and then calls fMRIPprep 1.4.1 docker to preprocess the structural and functional MRI data, which integrates FreeSurfer, ANTs, FSL and AFNI. With fMRIPprep, the data is processed into FreeSurfer fsaverage5 surface space and MNI volume space. DPABISurf further performs nuisance covariates regression (including ICA-AROMA) on the surface-based data (volume-based data is processed as well), and then calculate the commonly used R-fMRI metrics: amplitude of low frequency fluctuation (ALFF) (Zang et al., 2007), fractional ALFF (Zou et al., 2008), regional homogeneity (Zang et al., 2004), degree centrality (Zuo and Xing, 2014), and seed-based functional connectivity. DPABISurf also performs surface-based smoothing by calling FreeSurfer’s mri_surf2surf command. These processed metrics then enters surfaced-based statistical analyses within DPABISurf, which could perform surfaced-based permutation test with TFCE by integrating PALM. Finally, the corrected results could be viewed by the convenient surface viewer DPABISurf_VIEW, which is derived from spm_mesh_render.m.

DPABISurf is designed to make surface-based data analysis require minimum manual operations and almost no programming/scripting experience. We anticipate this open-source toolbox will assist novices and expert users alike and continue to support advancing R-fMRI methodology and its application to clinical translational studies.

DPABISurf is open-source and distributed under GNU/GPL, available with DPABI at http://www.rfmri.org/dpabi. It supports Windows 10 Pro, MacOS and Linux operating systems. You can run it with or without MATLAB.

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

 
New features of DPABISurf_V1.1_190725  (download at http://rfmri.org/dpabi):
1. New module for Surface-Based Temporal Dynamic Analysis (DPABI_TDA_Surf) was added. Dynamic regional indices (ALFF, fALFF, ReHo, Degree Centrality and Global Signal Correlation) and dynamic functional connectivity could be automatically calculated by one click through DPABI_TDA_Surf (with DPABISurf preprocessed data). The statistics maps (CV, Mean and SD) of the dynamic regional indices would also be generated by DPABI_TDA_Surf. A neuroimaging index which measures the concordance of the dynamic regional indices is incorporated into DPABI_TDA_Surf. Please see more details at: Yan, C.-G., Yang, Z., Colcombe, S.J., Zuo, X.-N., Milham, M.P., 2017. Concordance among indices of intrinsic brain function: insights from inter-individual variation and temporal dynamics. Sci Bull 62, 1572-1584.
2. The calculation of degree centrality now considers a vertex's correlation to both left and right hemispheres.
3. Standardization considers bilateral hemispheres. 
4. Smooth function after Standardization was added.
5. If ICA-AROMA was chosen, no head motion realign parameters would be regressed out.
6. Fixed compatibility issues with old matlab versions.
7. The default surface-based smoothing kernel changed to 6mm instead of 10mm.
8. The DPABISurf results organizing function was added to the R-fMRI Maps Project.
9. Output an excel table for the volume of subcortical structures (calculated by freesurfer): {WorkingDir}/Results/AnatVolu/Anat_Segment_Volume.tsv.
10. DPABISurf_VIEW, the surface-based viewer now has a function to yoke between different viewers.
11. Docker updated basing on fMRIPrep 1.4.1. Besides pull from docker hub, the docker file can be also downloaded form baidu (extract code: enmn).
12. Besides the stand alone version of DPABI (with GUI), the compiled version of DPABISurf_run was also added to docker. Users can run DPABISurf_run with scripting. 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
 
Tips for Linux or Mac O: please start matlab from terminal in order to reach docker in DPABI (e.g., Linux: matlab; Mac: open /Applications/MATLAB_R2018a.app/).

 

References:

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  • Cox, R.W. (1996). AFNI: software for analysis and visualization of functional magnetic resonance neuroimages. Comput Biomed Res, 29(3), 162-173.
  • Dale, A.M., Fischl, B., Sereno, M.I. (1999). Cortical surface-based analysis. I. Segmentation and surface reconstruction. Neuroimage, 9(2), 179-194, doi:10.1006/nimg.1998.0395.
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  • Yan, C.G., Wang, X.D., Zuo, X.N., Zang, Y.F. (2016). DPABI: Data Processing & Analysis for (Resting-State) Brain Imaging. Neuroinformatics, 14(3), 339-351, doi:10.1007/s12021-016-9299-4.
  • Zang, Y., Jiang, T., Lu, Y., He, Y., Tian, L. (2004). Regional homogeneity approach to fMRI data analysis. Neuroimage, 22(1), 394-400, doi:http://dx.doi.org/10.1016/j.neuroimage.2003.12.030.
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  • Zou, Q.-H., Zhu, C.-Z., Yang, Y., Zuo, X.-N., Long, X.-Y., Cao, Q.-J., Wang, Y.-F., Zang, Y.-F. (2008). An improved approach to detection of amplitude of low-frequency fluctuation (ALFF) for resting-state fMRI: Fractional ALFF. Journal of Neuroscience Methods, 172(1), 137-141, doi:http://dx.doi.org/10.1016/j.jneumeth.2008.04.012.
  • Zuo, X.-N., Xing, X.-X. (2014). Test-retest reliabilities of resting-state FMRI measurements in human brain functional connectomics: A systems neuroscience perspective. Neuroscience & Biobehavioral Reviews, 45, 100-118, doi:http://dx.doi.org/10.1016/j.neubiorev.2014.05.009.

 

Best,
Chao-Gan
 


--

Chao-Gan YAN, Ph.D.
Professor, Principal Investigator
Director, International Big-Data Center for Depression Research
Deputy Director, Magnetic Resonance Imaging Research Center
Institute of Psychology, Chinese Academy of Sciences
16 Lincui Road, Chaoyang District, Beijing 100101, China
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