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rsurfer (version 0.2)

Manipulating 'Freesurfer' Generated Data

Description

The software suite, 'Freesurfer', is a open-source software suite involving the segmentation of brain MRIs (see for more information). This package provides functionality to import the data generated by 'Freesurfer'; functions to easily manipulate the data; and provides brain specific normalisation commonly used when studying structural brain MRIs. This package has been designed using an installation of and data generated from 'Freesurfer' version 5.3.

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Version

Install

install.packages('rsurfer')

Monthly Downloads

7

Version

0.2

License

MIT + file LICENSE

Maintainer

Alexander Luke Spedding

Last Published

October 30th, 2017

Functions in rsurfer (0.2)

adni.setfiles

ADNI Set Files
caddementia.mergewithfreesurferoutput

CAD Dementia Merge With 'Freesurfer' Output
extract.brain.features

Extract All MRI Brain Features
extract.byname

Extract Features By Group Name
get.opposite.hemisphere.measurement

Get Opposite Hemisphere Measurement
getfieldgroup

Get Field Group of Feature
getnamesofvolumes

Get Names of Volumes
is.cortical

Is Feature Cortical
is.hippocampalvolume

Is Feature Hippocampal Volume
is.subcorticalvolume

Is Feature Subcortical Volume
subjectDistributionTableToLatex

Convert Subject Distribution Table To LaTeX
test.fieldextraction

Test Field Extraction
eliminateabnormalities

Eliminate Abnormal Rows and Columns
eliminateabnormalities.cols

Eliminate Abnormal Columns
extract.corticalvolumes

Extract Cortical Volumes
extract.hippocampalvolumes

Extract Hippocampal Volumes
fsdirectorycheck

'Freesurfer' Subject Directory Check
fsimport

'Freesurfer' Import (Serialise)
is.corticalarea

Is Feature Cortical Area
is.corticalthickness

Is Feature Cortical Thickness
isfsfeature

Is Feature Created by 'Freesurfer'
ixi.mergewithfreesurferoutput

'IXI' Merge Study Information With 'Freesurfer' Output
setfshome

Set 'Freesurfer' Home
subjectDistributionTable

Create Subject Distribution Table
caddementia.printfilelocations

CAD Dementia Print File Locations
caddementia.setfiles

CAD Dementia Set Files
extract.corticalthicknesses

Extract Cortical Thicknesses
extract.corticalthicknessstddevs

Extract Cortical Thickness Standard Deviations
generaterandomsubjects

Generate Random Subjects
get.hemisphere.side

Get Hemisphere Side
getfshome

Get 'Freesurfer' Home
getfsversion

Get 'Freesurfer' Version
normalise.listfieldgroups

List Normalisation Field Groups
normalise.listmethods

List Normalisation Methods
adni.mergewithfreesurferoutput

ADNI Merge With 'Freesurfer' Output
adni.printfilelocations

ADNI Print File Locations
eliminateabnormalities.rows

Eliminate Abnormal Rows
export.forKNIME

Export Data For KNIME
getnamesofareas

Get Names of Areas
getnamesofthicknesses

Get Names of Thicknesses
ixi.setfile

IXI Set File
normalise

Normalise
test.importing

Test Importing
test.normalisation

Test Normalisation
is.corticalthicknessstd

Is Feature Cortical Thickness Standard Deviation
is.corticalvolume

Is Feature Cortical Volume
searchforabnormalities.cols

Search For Abnormalities (Columns)
searchforabnormalities.rows

Search For Abnormalities (Rows)
addrandomdiagnosis

Add Random Diagnosis
addrandomgender

Add Random Gender
extract.cortical

Extract Cortical Fields
extract.corticalsurfaceareas

Extract Cortical Surface Areas
fsimport.listfields

'Freesurfer' Import (List Fields)
fsimport.serialise

'Freesurfer' Import (Serialise)
extract.subcorticalvolumes

Extract Subcortical Volumes
extract.volumes

Extract Cortical Thicknesses
removeabnormalrowsandcols

Remove Abnormalities
rsurfer-package

RSurfer