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Dear Colleagues,
We are pleased to announce the release of DPABISurf V1.2!
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 1.5.0 (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 V4.2 (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 1.5.0 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_V1.2_190919 within DPABI_V4.2_190919 (download at http://rfmri.org/dpabi, please also update the docker file by: docker pull cgyan/dpabi): 1. DPABISurf_V1.2_190919 updated. 1.1. A quality control module was added to DPABISurf. Now users can quality control surface reconstruction, EPI to T1 registration and T1 to MNI registration for all the subjects in one HTML file, respectively (based on fmriprep 1.5.0). For volume-based analysis, users can also generate group mask for DPABISurf, and exclude subjects by thresholding coverage and head motion. 1.2. DPABISurf now also output sulcus depth and volume in fsaverage and fsaverage5 spaces for statistical analysis. 1.3. In results organizer of DPABISurf, the redundant files would not be organized now. In addition, the fmriprep and freesurfer files were backed up, while excluding T1 image that may have privacy information such as face. 2. DPABI_VIEW has a new function "Surface View with DPABISurf_VIEW" now. This function will convert the files to fsaverage surface using freesurfer's mri_vol2surf command. Then the results were displayed by calling DPABISurf_VIEW to generate surface-based picture. Tips: 1) For Linux or Mac OS, please start matlab from terminal in order to reach docker in DPABI (e.g., Linux: matlab; Mac: open /Applications/MATLAB_R2018a.app/). 2) Before running DPABISurf_Pipeline, you can test the docker environment by running DPABI->DPABISurf->Utilities->Volume-Surface Projector. If the file can be successfully projected to surface, then the software is all set.
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Best,
Chao-Gan