automated anatomical labeling (aal) atlas  (MathWorks Inc)

Journal: Scientific Reports

Article Title: Probabilistic comparison of gray and white matter coverage between depth and surface intracranial electrodes in epilepsy

doi: 10.1038/s41598-021-03414-5

Figure Lengend Snippet: Overview of Methods. ( A ) The processing pipeline used patient specific imaging. All patients were processed through LeGUI, FreeSurfer, and SIMNIBS, while only surface electrode patients received extra processing to project the electrodes to the smoothed gray matter surface as well as left and right hemisphere segmentation for interhemispheric contacts. Overlap of gray and white matter segmentations with RoIs were used to calculate volumes of gray and white matter coverage. A subset of patients were used to run FEM-based RoIs. Reported sample sizes indicate the number of patients included in each implant category. ( B ) Electrode localization was performed in the freely available LeGUI software to mark strip, grid, and depth electrodes across a cohort of 65 patients. LeGUI automatically processes probabilistic gray and white matter segmentations and numerous atlas registrations including the AAL and NMM atlases. ( C ) Substantial brain shift is frequently observed in subdural electrode cases during surgical implantation. After image co-registration, the subdural electrodes localized from the CT may appear inside of the brain (yellow) rather than on top of the cortical surface. ( D ) All subdural electrodes were projected (yellow—original location, black—projected location) onto the smooth gray matter surface according to Hermes et al., 2010. ( E ) In patients with interhemispheric subdural electrodes, the left and right hemisphere segmentations were created in FreeSurfer so that volumes would be restricted to the hemisphere from which the electrode recorded neural activity. ( F ) Spheres at fixed radii from 1–15 mm at 0.5 mm steps were placed at the contact centroids. 10 mm RoIs are shown in blue. Overlap of spherical volumes with gray and white matter segmentations quantify the amount of gray and white matter coverage for different modalities.

Article Snippet: Patient structural imaging was nonlinearly registered to the Neuromorphometrics (NMM) brain atlas and Macroscopic Parcellations of the AAL brain atlas (Neuromorphometrics, Inc., http://neuromorphometrics.com/ , ).

Techniques: Imaging, Software, Stripping Membranes, Activity Assay

Journal: Diagnostics

Article Title: Impact of Pretreatment Ischemic Location on Functional Outcome after Thrombectomy

doi: 10.3390/diagnostics11112038

Figure Lengend Snippet: Workflow of lesion location determination: (1) Ischemic lesions were segmented semi-automatically. (2) The generated lesion masks were then normalized to standard Montreal Neurological Institute space using SPM12. (3) The regional ischemic location was determined according to Automated Anatomical Labeling Atlas and the Johns Hopkins University White Matter Labels (1 mm) Atlas. Abbreviations: MNI = Montreal Neurological Institute; AAL = Automated Anatomical Labeling Atlas; JHU-WM = Johns Hopkins University White Matter Labels (1 mm) Atlas.

Article Snippet: Regional ischemic location was determined according to the Automated Anatomical Labeling (AAL) Atlas (as gray matter atlas) and the Johns Hopkins University White Matter Labels (1 mm) (JHU-WM) Atlas (for white matter tracks) available in the MRIcron software package ( http://people.cas.sc.edu/rorden/mricron/index.html (version released on August 2014) (accessed on 30 October 2019)) [ ].

Techniques: Generated, Labeling

Journal: medRxiv

Article Title: Probabilistic comparison of gray and white matter coverage between depth and surface intracranial electrodes in epilepsy: a patient-specific modeling and empirical study

doi: 10.1101/2021.08.04.21261603

Figure Lengend Snippet: Overview of Methods. A . The processing pipeline used patient specific imaging. All patients were processed through LeGUI, FreeSurfer, and SIMNIBS, while only surface electrode patients received extra processing to project the electrodes to the smoothed gray matter surface as well as left and right hemisphere segmentation for interhemispheric contacts. Overlap of gray and white matter segmentations with RoIs were used to calculate volumes of gray and white matter coverage. A subset of patients were used to run FEM-based RoIs. Reported sample sizes indicate the number of patients included in each implant category. B . Electrode localization was performed in the freely available LeGUI software to mark strip, grid, and depth electrodes across a cohort of 65 patients. LeGUI automatically processes probabilistic gray and white matter segmentations and numerous atlas registrations including the AAL and NMM atlases. C . Substantial brain shift is frequently observed in subdural electrodes cases during surgical implantation. After image co-registration, the subdural electrodes localized from the CT may appear inside of the brain (yellow) rather than on top of the cortical surface. D . All subdural electrodes were projected (yellow – original location, black – projected location) onto the smooth gray matter surface according to Hermes et al., 2010. E . In patients with interhemispheric subdural electrodes, the left and right hemisphere segmentations were created in FreeSurfer so that volumes would be restricted to the hemisphere from which the electrode recorded neural activity. F . Spheres at fixed radii from 1-15 mm at 0.5 mm steps were placed at the contact centroids. 10 mm RoIs are shown in blue. Overlap of spherical volumes with gray and white matter segmentations quantify the amount of gray and white matter coverage for different modalities.

Article Snippet: Patient structural imaging was nonlinearly registered to the Neuromorphometrics (NMM) brain atlas and Macroscopic Parcellations of the AAL brain atlas (Neuromorphometrics, Inc., http://neuromorphometrics.com/ , [ , ]).

Techniques: Imaging, Software, Stripping Membranes, Activity Assay