Journal: Journal of neural engineering

Article Title: Realistic volumetric-approach to simulate transcranial electric stimulation—ROAST—a fully automated open-source pipeline

doi: 10.1088/1741-2552/ab208d

Figure Lengend Snippet: Candidate pipelines for building a current-flow model of the head. The input is the MRI of an individual, and the output of each pipeline is the predicted electric field distribution. The different pipelines we are evaluating are ROAST, with its variants (ROAST-sg, ROAST-sa, ROAST-gg), three different segmentation options in SimNIBS (SimNIBS-hr, SimNIBS-hrE and SimNIBS-mm), and the approach published in Huang et al (2017) . Data from different methods at different stages in these pipelines are used for comparison, as indicated by the black dots on the dashed vertical lines: / —comparing segmentation; —comparing electric field distribution; —validating each pipeline using actual recordings.

Article Snippet: The 5th to 7th pipelines in are three different segmentation options in SimNIBS (Version 2.1): headreco (SimNIBS-hr), headreco with CAT12 toolbox (denoted SimNIBS-hrE here) and mri2mesh (SimNIBS-mm) ( Windhoff et al 2011 , Nielsen et al 2018 ).

Techniques: Comparison

Journal: Journal of neural engineering

Article Title: Realistic volumetric-approach to simulate transcranial electric stimulation—ROAST—a fully automated open-source pipeline

doi: 10.1088/1741-2552/ab208d

Figure Lengend Snippet: Segmented head tissues from each modeling software that are compared. Refer to figure 1 for details on each pipeline. WM: white matter; GM: gray matter; CSF: cerebrospinal fluid.

Article Snippet: The 5th to 7th pipelines in are three different segmentation options in SimNIBS (Version 2.1): headreco (SimNIBS-hr), headreco with CAT12 toolbox (denoted SimNIBS-hrE here) and mri2mesh (SimNIBS-mm) ( Windhoff et al 2011 , Nielsen et al 2018 ).

Techniques: Software

Journal: Journal of neural engineering

Article Title: Realistic volumetric-approach to simulate transcranial electric stimulation—ROAST—a fully automated open-source pipeline

doi: 10.1088/1741-2552/ab208d

Figure Lengend Snippet: Example brain slices (A1), (A2) and 3D renderings (B)–(D) showing the segmentation from different software tools (ROAST, SimNIBS-hr, SimNIBS-hrE, SimNIBS-mm) and the manual segmentation (Manual) of the individual head S1. For the 3D renderings, both the volumetric (vol) and surface (surf) formats are displayed for the CSF and skull generated by SimNIBS-hr. Red arrows indicate the optic foramen and the foramen magnum. Note that SimNIBS-mm is missing portions of midbrain and spinal cord due to is limited FOV. Refer to for the details of the four segmentation methods.

Article Snippet: The 5th to 7th pipelines in are three different segmentation options in SimNIBS (Version 2.1): headreco (SimNIBS-hr), headreco with CAT12 toolbox (denoted SimNIBS-hrE here) and mri2mesh (SimNIBS-mm) ( Windhoff et al 2011 , Nielsen et al 2018 ).

Techniques: Software, Generated

Journal: eLife

Article Title: Chimpanzee brain morphometry utilizing standardized MRI preprocessing and macroanatomical annotations

doi: 10.7554/eLife.60136

Figure Lengend Snippet:

Article Snippet: To illustrate the structural processing pipeline, we have created exemplar MATLAB SPM batch scripts that utilizes the Juna.Chimp templates in CAT12’s preprocessing workflow to conduct segmentation, spatial registration, and finally some basic age analysis on an openly available direct-to-download chimpanzee sample ( http://www.chimpanzeebrain.org/ ).

Techniques: Software