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DPABISurf

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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. Please go to http://www.rfmri.org/dpabi to download DPABI.
    2. Add with subfolders for DPABI in MATLAB's path setting.
    3. Input 'dpabi' and then follow the instructions of the “Install” Button on DPABISurf.
  2. Without MATLAB.
    1. Install Docker.
    2. Terminal:
       docker pull cgyan/dpabi 
    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).

    4. Open VNC Viewer, connect to localhost:5925, the password is 'dpabi'.
    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!

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.
  Esteban, O., Markiewicz, C.J., Blair, R.W., Moodie, C.A., Isik, A.I., Erramuzpe, A., Kent, J.D., Goncalves, M., DuPre, E., Snyder, M., Oya, H., Ghosh, S.S., Wright, J., Durnez, J., Poldrack, R.A., Gorgolewski, K.J. (2018). fMRIPrep: a robust preprocessing pipeline for functional MRI. Nat Methods, doi:10.1038/s41592-018-0235-4.
  Gorgolewski, K.J., Auer, T., Calhoun, V.D., Craddock, R.C., Das, S., Duff, E.P., Flandin, G., Ghosh, S.S., Glatard, T., Halchenko, Y.O., Handwerker, D.A., Hanke, M., Keator, D., Li, X., Michael, Z., Maumet, C., Nichols, B.N., Nichols, T.E., Pellman, J., Poline, J.B., Rokem, A., Schaefer, G., Sochat, V., Triplett, W., Turner, J.A., Varoquaux, G., Poldrack, R.A. (2016). The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Sci Data, 3, 160044, doi:10.1038/sdata.2016.44.
  Jenkinson, M., Bannister, P., Brady, M., Smith, S. (2002). Improved optimization for the robust and accurate linear registration and motion correction of brain images. Neuroimage, 17(2), 825-841.
  Tange, O. (2011). Gnu parallel-the command-line power tool. The USENIX Magazine, 36(1), 42-47.
  Winkler, A.M., Ridgway, G.R., Douaud, G., Nichols, T.E., Smith, S.M. (2016). Faster permutation inference in brain imaging. Neuroimage, 141, 502-516, doi:10.1016/j.neuroimage.2016.05.068.
  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.
  Zang, Y.F., He, Y., Zhu, C.Z., Cao, Q.J., Sui, M.Q., Liang, M., Tian, L.X., Jiang, T.Z., Wang, Y.F. (2007). Altered baseline brain activity in children with ADHD revealed by resting-state functional MRI. Brain Dev, 29(2), 83-91, doi:10.1016/j.braindev.2006.07.002.
  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.

Organizar archivos

$ mkdir dpabi
$ cd dpabi
$ mkdir FunImg
$ for x in ../fmri/smc0*.nii.gz; do n=$(echo ${x} | sed 's/..\/fmri\/smc0\(.*\)s.*\.nii\.gz/\1/' ) a=$(echo ${x} | sed 's/..\/fmri\/smc0\(.*\)s\(.*\)\.nii\.gz/Subject\1\/s\2smc\1.nii.gz/'); mkdir FunImg/Subject${n}; imcp ${x} FunImg/${a}; done
$ mkdir T1Img
$ for x in ../mri/smc0*.nii.gz; do n=$(echo ${x} | sed 's/..\/mri\/smc0\(.*\)s.*\.nii\.gz/\1/' ) a=$(echo ${x} | sed 's/..\/mri\/smc0\(.*\)s\(.*\)\.nii\.gz/Subject\1\/s\2smc\1.nii.gz/'); mkdir T1Img/Subject${n}; imcp ${x} T1Img/${a}; done

PUF, esto no funciona bien con nifti, hay que hacerlo desde los dicom a ver que pasa.

[osotolongo@detritus dpabi]$ mkdir FunRaw
[osotolongo@detritus dpabi]$ mkdir T1Raw
[osotolongo@detritus dpabi]$ for x in /nas/corachan/facehbi/*; do for y in ${x}/*; do if [[ `dckey -k "SeriesDescription" ${y}/Img00001.dcm 2>&1 | grep t1_mprage` ]]; then ddir=$(echo ${y} | sed 's/.*F\(.*\)\/Serie.*/Subject\1/'); echo ${ddir}; mkdir T1Raw/${ddir}; for img in ${y}/*; do destd=$(echo ${img} | sed 's/.*\/F\(.*\)\/Serie(\(.*\))\//Subject\1\/s\2_/'); cp ${img} T1Raw/${destd}; done; fi; done; done
[osotolongo@detritus dpabi]$ for x in /nas/corachan/facehbi/*; do for y in ${x}/*; do if [[ `dckey -k "SeriesDescription" ${y}/Img00001.dcm 2>&1 | grep ep2d_pace_moco_p2` ]]; then ddir=$(echo ${y} | sed 's/.*F\(.*\)\/Serie.*/Subject\1/'); echo ${ddir}; mkdir FunRaw/${ddir}; for img in ${y}/*; do destd=$(echo ${img} | sed 's/.*\/F\(.*\)\/Serie(\(.*\))\//Subject\1\/s\2_/'); cp ${img} FunRaw/${destd}; done; fi; done; done
neuroimagen/dpabi.txt · Last modified: 2020/08/04 10:58 (external edit)