Software available in NeuGRID2 

NeuGRID2 offers a range of applications and computational resources.
In the table below you will find a list of software currently available on neuGRID2. The list is updated periodically based on users’ requests.

 


FreeSurfer v5.3 (Recon all)

Clinical/Biological Phenomenon of study:
Study of hippocampal anatomy. Hippocampal volumes in template space (MNI) are contrasted against a normative population of 200 healthy control subjects.
Description:
Freesurfer is a set of automated tools for reconstruction of the hippocampus (together with other brain’s cortical areas and subcortical brain structures from MRI data).
Resources required:
2GB, 1 day, single core


FreeSurfer v6.0 (Recon all)

Clinical/Biological Phenomenon of study:
Study of the main cortical and subcortical regions: hippocampal, amygdala, ventricle, thalamus, basal ganglia, whole brain volumes and temporal cortex atrophy. These variables are contrasted against a normative population of 532 healthy control subjects. All values are normalized on TIV.
Description:
Freesurfer is a set of automated tools for reconstruction of the brain’s cortical areas and subcortical brain structures from MRI data.
Resources required:
2GB, 1 day, single core


Adaboost (ICBM152)

Clinical/Biological Phenomenon of study:
AdaBoost is a machine learning method that is used to segment hippocampus regions from 3D T1-weighted structural brain Magnetic Resonance (MR) scans. This has been made possible thanks to the support of the following contributors: Paul Thompson (USC) and DECIDE initiative. Hippocampal volumes are contrasted against a normative population of 200 healthy control subjects. Volumes obtained are in template (ICBM152) space.
Description:
Hippocampal volume segmentation.
Resources required:
2GB, 1 hour, single core.


Adaboost (native space)

Clinical/Biological Phenomenon of study:
AdaBoost is a machine learning method that is used to segment hippocampus regions from 3D T1-weighted structural brain Magnetic Resonance (MR) scans. This has been made possible thanks to the support of the following contributors: Paul Thompson (USC) and DECIDE initiative. Hippocampal volumes are contrasted against a normative population of 421 healthy control subjects. Volumes obtained are in native space. All values are normalized on TIV computed using SPM12.
Description:
Hippocampal volume segmentation.
Resources required:
2GB, 1 hour, single core.


HCI

Clinical/Biological Phenomenon of study:
HCI is an AD-related hypometabolic convergence index. HCI has been shown able to discriminate patients with clinical AD from healthy older persons. This has been made possible thanks to the support of the following contributors: Kewei Chen and Eric Reiman (Banner Alzheimer’s Institute, Phoenix).
Description:
Brain hypometabolism.
Resources required:
1GB, 1 hour, single core.


METAROI

Clinical/Biological Phenomenon of study:
MetaROI is an average metabolism index computed on a set of analytically derived regions of interest (i.e.: left angular, right angular, left temporal, right temporal, and bilateral posterior cingulate binary masks in Montreal Neurological Institute space) reflecting AD hypometabolism pattern. MetaROI index is normalized using the pons and cerebellar vermis ROIs in MNI space. MetaROI has been shown sensitive in the detection of longitudinal cognitive and functional changes in AD and MCI patients. This has been made possible thanks to the support of the following contributor: William Jagust (UC Berkeley & Lawrence Berkeley National Laboratory, California).
Description:
Brain hypometabolism.
Resources required:
1GB, 1 hour, single core.


LPA

Clinical/Biological Phenomenon of study:
Quantification of the T2 hyperintense lesions in FLAIR images. Volumes (in ml) are contrasted against a normative population of 900 subjects.
Description:
White Matter segmentation.
Resources required:
0.5 GB, 1 hour, single core.