interface

BEN interface

Codes for neuroimaging analysis via Matlab, Python(Nipype) and shell scripting.

As skull stripping is usually the first preprocessing step in the most pipelines, BEN can be used as a tool independently or called in shell scripts to work with other neuroimaging tool synergistically.

Usage

Please refer to the Colab notebook examples.

Neuroimaging tool	Style	Colab link
ANTs (Registration)	Shell scripts	Sec 3.0
ANTs (N4)	Python(Nipype)

File structure

tree
│  
├─matlab
│      BEN-skull-strippting.m
│      README.md
│      spm-ben.m
│      
├─python
│      cli.py
│      dmri_camino_dti.py
│      dmri_connectivity.py
│      dmri_connectivity_advanced.py
│      dmri_dtk_dti.py
│      dmri_dtk_odf.py
│      dmri_fsl_dti.py
│      dmri_group_connectivity_camino.py
│      dmri_group_connectivity_mrtrix.py
│      dmri_mrtrix_dti.py
│      dmri_preprocessing.py
│      dmri_tbss_nki.py
│      fmri_ants_openfmri.py
│      fmri_freesurfer_smooth.py
│      fmri_fsl.py
│      fmri_fsl_feeds.py
│      fmri_fsl_reuse.py
│      fmri_nipy_glm.py
│      fmri_openfmri.py
│      fmri_slicer_coregistration.py
│      fmri_spm.py
│      fmri_spm_auditory.py
│      fmri_spm_dartel.py
│      fmri_spm_face.py
│      fmri_spm_nested.py
│      howto_caching_example.py
│      README.md
│      rsfmri_vol_surface_preprocessing.py
│      rsfmri_vol_surface_preprocessing_nipy.py
│      smri_antsregistration_build_template.py
│      smri_ants_build_template.py
│      smri_ants_registration.py
│      smri_cbs_skullstripping.py
│      smri_freesurfer.py
│      smri_fsreconall.py
│      tessellation_tutorial.py
│      test_spm.py
│      utils_ants_os.py
│      utils_trans_os.py
│      workshop_dartmouth_2010.py
│      
└─shell_sript
        afni_proc.sh
        ants_registration.sh
        BEN-skull-strippting.sh
        freesurfer_recon-all.sh
        fsl_dti_tracking.sh
        fsl_registrision.sh
        README.md
        spm.sh