fslpy
3.0.1
fslpy
fsl
Contributing to
fslpy
fslpy
release history
fslpy
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Index
Index
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
A
abs() (fsl.wrappers.fslmaths.fslmaths method)
absolute() (fsl.transform.nonlinear.DeformationField property)
add() (fsl.wrappers.fslmaths.fslmaths method)
add_to_parser() (fsl.utils.fslsub.SubmitParams class method)
addAtlas() (fsl.data.atlases.AtlasRegistry method)
(in module fsl.data.atlases)
addComponent() (fsl.data.volumelabels.VolumeLabels method)
addExt() (in module fsl.data.image)
(in module fsl.utils.path)
addLabel() (fsl.data.volumelabels.VolumeLabels method)
addVertexData() (fsl.data.mesh.Mesh method)
addVertices() (fsl.data.mesh.Mesh method)
adjust() (fsl.data.image.Nifti method)
adjustCoverage() (in module fsl.data.imagewrapper)
all_variables() (fsl.utils.filetree.filetree.FileTree property)
allFiles() (in module fsl.utils.path)
ALLOWED_EXTENSIONS (in module fsl.data.gifti)
(in module fsl.data.image)
(in module fsl.data.mghimage)
(in module fsl.data.vtk)
allowErrors() (fsl.utils.idle.IdleLoop property)
allVariables() (in module fsl.utils.filetree.query)
append_variables() (fsl.utils.filetree.utils.Optional method)
(fsl.utils.filetree.utils.Part method)
(fsl.utils.filetree.utils.Required method)
applyArgStyle() (in module fsl.wrappers.wrapperutils)
applyDeformation() (in module fsl.transform.nonlinear)
applyLinear() (in module fsl.scripts.fsl_apply_x5)
applyNonlinear() (in module fsl.scripts.fsl_apply_x5)
applySmoothing() (in module fsl.utils.image.resample)
applytopup() (in module fsl.wrappers.eddy)
applywarp() (in module fsl.wrappers.fnirt)
applyxfm() (in module fsl.wrappers.flirt)
applyxfm4D() (in module fsl.wrappers.flirt)
architecture (fsl.utils.fslsub.SubmitParams attribute)
as_flags() (fsl.utils.fslsub.SubmitParams method)
asDeformationField() (fsl.transform.nonlinear.CoefficientField method)
asImage() (fsl.data.bitmap.Bitmap method)
assertFileExists() (in module fsl.utils.assertions)
assertIsFuncGifti() (in module fsl.utils.assertions)
assertIsMelodicDir() (in module fsl.utils.assertions)
assertIsNifti() (in module fsl.utils.assertions)
assertIsNifti3D() (in module fsl.utils.assertions)
assertIsNifti4D() (in module fsl.utils.assertions)
assertIsSurfGifti() (in module fsl.utils.assertions)
assertNiftiShape() (in module fsl.utils.assertions)
Atlas (class in fsl.data.atlases)
Atlas() (in module fsl.utils.parse_data)
AtlasDescription (class in fsl.data.atlases)
AtlasLabel (class in fsl.data.atlases)
atlasOrDesc() (in module fsl.scripts.atlasq)
atlasquery_emulation() (in module fsl.scripts.atlasq)
AtlasRegistry (class in fsl.data.atlases)
axes() (fsl.utils.filetree.query.FileTreeQuery method)
axisAnglesToRotMat() (in module fsl.transform.affine)
axisBounds() (in module fsl.transform.affine)
axisMapping() (fsl.data.image.Nifti method)
B
BasisFunctionEV (class in fsl.data.featdesign)
bet() (in module fsl.wrappers.bet)
BIDSFile (class in fsl.utils.bids)
bin() (fsl.wrappers.fslmaths.fslmaths method)
binv() (fsl.wrappers.fslmaths.fslmaths method)
Bitmap (class in fsl.data.bitmap)
BITMAP_DESCRIPTIONS (in module fsl.data.bitmap)
BITMAP_EXTENSIONS (in module fsl.data.bitmap)
block() (in module fsl.utils.idle)
bounds() (fsl.data.mesh.Mesh property)
bptf() (fsl.wrappers.fslmaths.fslmaths method)
C
Cache (class in fsl.utils.cache)
CacheItem (class in fsl.utils.cache)
calcExpansion() (in module fsl.data.imagewrapper)
calcFaceNormals() (in module fsl.data.mesh)
calcRange() (fsl.data.image.Image method)
calcVertexNormals() (in module fsl.data.mesh)
callRate() (fsl.utils.idle.IdleLoop property)
cancelIdle() (fsl.utils.idle.IdleLoop method)
canHaveGui() (fsl.utils.platform.Platform property)
canonicalShape() (in module fsl.data.image)
canonicalSliceObj() (in module fsl.data.imagewrapper)
check_forbidden_characters() (in module fsl.utils.filetree.parse)
clear() (fsl.data.volumelabels.VolumeLabels method)
(fsl.utils.cache.Cache method)
(fsl.utils.settings.Settings method)
(in module fsl.utils.settings)
clearComponents() (fsl.data.volumelabels.VolumeLabels method)
clearLabels() (fsl.data.volumelabels.VolumeLabels method)
clearVertexData() (fsl.data.mesh.Mesh method)
cluster() (in module fsl.wrappers.misc)
clusterResults() (fsl.data.featimage.FEATImage method)
cmd_line_flags (fsl.utils.fslsub.SubmitParams attribute)
cmdwrapper() (in module fsl.wrappers.wrapperutils)
CoefficientField (class in fsl.transform.nonlinear)
coefficientFieldToDeformationField() (in module fsl.transform.nonlinear)
collapseExpansions() (in module fsl.data.imagewrapper)
commonBase() (in module fsl.utils.path)
compareVersions() (in module fsl.data.dicom)
(in module fsl.version)
componentsToEigendecomposition() (in module fsl.data.dtifit)
componentsToTensor() (in module fsl.data.dtifit)
compose() (in module fsl.transform.affine)
concat() (in module fsl.transform.affine)
concatxfm() (in module fsl.wrappers.flirt)
configDir() (fsl.utils.settings.Settings property)
configID() (fsl.utils.settings.Settings property)
ConfoundEV (class in fsl.data.featdesign)
contains_optionals() (fsl.utils.filetree.utils.Optional method)
(fsl.utils.filetree.utils.Part method)
contrastNames() (fsl.data.featimage.FEATImage method)
contrasts() (fsl.data.featimage.FEATImage method)
convertDeformationSpace() (in module fsl.transform.nonlinear)
convertDeformationType() (in module fsl.transform.nonlinear)
convertwarp() (in module fsl.wrappers.fnirt)
coordLabel() (fsl.data.atlases.LabelAtlas method)
coordQuery() (in module fsl.scripts.atlasq)
coordValues() (fsl.data.atlases.StatisticAtlas method)
CORE_GEOMETRY_DESCRIPTIONS (in module fsl.data.freesurfer)
CORE_GEOMETRY_FILES (in module fsl.data.freesurfer)
coverage() (fsl.data.imagewrapper.ImageWrapper method)
covered() (fsl.data.imagewrapper.ImageWrapper property)
CRC_DCM2NIIX_VERSION (in module fsl.data.dicom)
createLock (fsl.utils.idle.MutexFactory attribute)
D
data() (fsl.data.bitmap.Bitmap property)
(fsl.data.image.Image property)
dataRange() (fsl.data.image.Image property)
(fsl.data.imagewrapper.ImageWrapper property)
dataSource() (fsl.data.bitmap.Bitmap property)
(fsl.data.image.Image property)
(fsl.data.mesh.Mesh property)
decompose() (in module fsl.transform.affine)
decomposeTensorMatrix() (in module fsl.data.dtifit)
deepest() (in module fsl.utils.path)
DEFAULT_TOPIC (in module fsl.utils.notifier)
defaultExt() (in module fsl.data.image)
defines() (fsl.utils.filetree.filetree.FileTree method)
DeformationField (class in fsl.transform.nonlinear)
deformationType() (fsl.transform.nonlinear.DeformationField property)
delete() (fsl.utils.settings.Settings method)
(in module fsl.utils.settings)
deleteFile() (fsl.utils.settings.Settings method)
(in module fsl.utils.settings)
deprecated() (in module fsl.utils.deprecated)
dequeue() (fsl.utils.idle.TaskThread method)
deregister() (fsl.utils.notifier.Notifier method)
detectDeformationType() (in module fsl.transform.nonlinear)
determineAffine() (fsl.data.image.Nifti static method)
determineShape() (fsl.data.image.Nifti static method)
dicomDir() (fsl.data.dicom.DicomImage property)
DicomImage (class in fsl.data.dicom)
dilF() (fsl.wrappers.fslmaths.fslmaths method)
dilM() (fsl.wrappers.fslmaths.fslmaths method)
disable() (fsl.utils.notifier.Notifier method)
disableAll() (fsl.utils.notifier.Notifier method)
disabled() (in module fsl.utils.assertions)
displacements() (fsl.transform.nonlinear.CoefficientField method)
div() (fsl.wrappers.fslmaths.fslmaths method)
doFlirt() (in module fsl.scripts.fsl_convert_x5)
doFnirt() (in module fsl.scripts.fsl_convert_x5)
DRY_RUN (in module fsl.utils.run)
dryrun() (in module fsl.utils.run)
DTIFitTensor (class in fsl.data.dtifit)
dtype() (fsl.data.image.Image property)
E
eddy_cuda() (in module fsl.wrappers.eddy)
eigendecompositionToComponents() (in module fsl.data.dtifit)
eigendecompositionToTensor() (in module fsl.data.dtifit)
email (fsl.utils.fslsub.SubmitParams attribute)
enable() (fsl.utils.notifier.Notifier method)
enableAll() (fsl.utils.notifier.Notifier method)
enabled() (in module fsl.data.dicom)
enqueue() (fsl.utils.idle.TaskThread method)
ensureIsImage() (in module fsl.utils.ensure)
env (fsl.utils.fslsub.SubmitParams attribute)
ero() (fsl.wrappers.fslmaths.fslmaths method)
EV (class in fsl.data.featdesign)
evNames() (fsl.data.featimage.FEATImage method)
expectedShape() (in module fsl.data.imagewrapper)
Expired
EXTENSION_DESCRIPTIONS (in module fsl.data.gifti)
(in module fsl.data.image)
(in module fsl.data.mghimage)
(in module fsl.data.vtk)
EXTRA_GEOMETRY_FILES (in module fsl.data.freesurfer)
extra_tree_dirs() (in module fsl.utils.filetree.parse)
extract_variables() (fsl.utils.filetree.filetree.FileTree method)
(fsl.utils.filetree.utils.Template method)
(in module fsl.utils.filetree.utils)
F
fast() (in module fsl.wrappers.fast)
FEATFSFDesign (class in fsl.data.featdesign)
FEATImage (class in fsl.data.featimage)
fieldToRefMat() (fsl.transform.nonlinear.CoefficientField property)
fieldType() (fsl.transform.nonlinear.CoefficientField property)
FILE_GROUPS (in module fsl.data.image)
filename() (fsl.data.featdesign.VoxelwiseEVMixin property)
(fsl.utils.filetree.query.Match property)
fileOrArray() (in module fsl.wrappers.wrapperutils)
fileOrImage() (in module fsl.wrappers.wrapperutils)
fileOrText() (in module fsl.wrappers.wrapperutils)
FileOrThing (class in fsl.wrappers.wrapperutils)
FileOrThing.Results (class in fsl.wrappers.wrapperutils)
filePath() (fsl.utils.settings.Settings method)
(in module fsl.utils.settings)
FileTree (class in fsl.utils.filetree.filetree)
FileTreeQuery (class in fsl.utils.filetree.query)
fill_known() (fsl.utils.filetree.utils.Optional method)
(fsl.utils.filetree.utils.Part method)
(fsl.utils.filetree.utils.Required method)
(fsl.utils.filetree.utils.Template method)
fillh() (fsl.wrappers.fslmaths.fslmaths method)
find() (fsl.data.atlases.Atlas method)
(fsl.data.atlases.AtlasDescription method)
find_variables() (in module fsl.utils.filetree.utils)
findReferenceImage() (in module fsl.data.freesurfer)
(in module fsl.data.vtk)
fit() (fsl.data.featimage.FEATImage method)
fixExt() (in module fsl.data.image)
flags (fsl.utils.fslsub.SubmitParams attribute)
flirt() (in module fsl.wrappers.flirt)
flirtMatrixToSform() (in module fsl.transform.flirt)
flirtToX5() (in module fsl.scripts.fsl_convert_x5)
floatlist() (in module fsl.scripts.resample_image)
fnirt() (in module fsl.wrappers.fnirt)
fnirtToX5() (in module fsl.scripts.fsl_convert_x5)
FreesurferMesh (class in fsl.data.freesurfer)
from_args() (fsl.utils.fslsub.SubmitParams class method)
fromFlirt() (in module fsl.transform.flirt)
fromFnirt() (in module fsl.transform.fnirt)
frozen() (fsl.utils.platform.Platform property)
FSFError
fsl
module
fsl.data
module
fsl.data.atlases
module
fsl.data.bitmap
module
fsl.data.constants
module
fsl.data.dicom
module
fsl.data.dtifit
module
fsl.data.featanalysis
module
fsl.data.featdesign
module
fsl.data.featimage
module
fsl.data.fixlabels
module
fsl.data.freesurfer
module
fsl.data.gifti
module
fsl.data.image
module
fsl.data.imagewrapper
module
fsl.data.melodicanalysis
module
fsl.data.melodicimage
module
fsl.data.mesh
module
fsl.data.mghimage
module
fsl.data.utils
module
fsl.data.vest
module
fsl.data.volumelabels
module
fsl.data.vtk
module
fsl.scripts
module
fsl.scripts.atlasq
module
fsl.scripts.fsl_apply_x5
module
fsl.scripts.fsl_convert_x5
module
fsl.scripts.fsl_ents
module
fsl.scripts.imcp
module
fsl.scripts.imglob
module
fsl.scripts.immv
module
fsl.scripts.resample_image
module
fsl.transform
module
fsl.transform.affine
module
fsl.transform.flirt
module
fsl.transform.fnirt
module
fsl.transform.nonlinear
module
fsl.transform.x5
module
fsl.utils
module
fsl.utils.assertions
module
fsl.utils.bids
module
fsl.utils.cache
module
fsl.utils.deprecated
module
fsl.utils.ensure
module
fsl.utils.filetree
module
fsl.utils.filetree.filetree
module
fsl.utils.filetree.parse
module
fsl.utils.filetree.query
module
fsl.utils.filetree.utils
module
fsl.utils.fslsub
module
fsl.utils.idle
module
fsl.utils.image
module
fsl.utils.image.resample
module
fsl.utils.image.roi
module
fsl.utils.imcp
module
fsl.utils.memoize
module
fsl.utils.meta
module
fsl.utils.naninfrange
module
fsl.utils.notifier
module
fsl.utils.parse_data
module
fsl.utils.path
module
fsl.utils.platform
module
fsl.utils.run
module
fsl.utils.settings
module
fsl.utils.tempdir
module
fsl.utils.weakfuncref
module
fsl.version
module
fsl.wrappers
module
fsl.wrappers.bet
module
fsl.wrappers.eddy
module
fsl.wrappers.fast
module
fsl.wrappers.flirt
module
fsl.wrappers.fnirt
module
fsl.wrappers.fsl_anat
module
fsl.wrappers.fslmaths
module
fsl.wrappers.fugue
module
fsl.wrappers.melodic
module
fsl.wrappers.misc
module
fsl.wrappers.wrapperutils
module
fsl_anat() (in module fsl.wrappers.fsl_anat)
FSL_PREFIX (in module fsl.utils.run)
fsl_regfilt() (in module fsl.wrappers.melodic)
fsldevdir() (fsl.utils.platform.Platform property)
fsldir() (fsl.utils.platform.Platform property)
fslmaths (class in fsl.wrappers.fslmaths)
FSLNotPresent
fslreorient2std() (in module fsl.wrappers.misc)
fslroi() (in module fsl.wrappers.misc)
fslVersion() (fsl.utils.platform.Platform property)
fslwrapper() (in module fsl.wrappers.wrapperutils)
fugue() (in module fsl.wrappers.fugue)
full_name() (fsl.utils.filetree.query.Match property)
func_to_cmd() (in module fsl.utils.fslsub)
function() (fsl.utils.weakfuncref.WeakFunctionRef method)
G
genComponentIndexList() (in module fsl.scripts.fsl_ents)
generateAffines() (fsl.data.image.Nifti static method)
get() (fsl.data.atlases.LabelAtlas method)
(fsl.data.atlases.StatisticAtlas method)
(fsl.utils.cache.Cache method)
(fsl.utils.filetree.filetree.FileTree method)
get_all() (fsl.utils.filetree.filetree.FileTree method)
(fsl.utils.filetree.utils.Template method)
(in module fsl.utils.filetree.utils)
get_all_trees() (fsl.utils.filetree.filetree.FileTree method)
get_all_vars() (fsl.utils.filetree.filetree.FileTree method)
get_registered() (in module fsl.utils.filetree.filetree)
get_template() (fsl.utils.filetree.filetree.FileTree method)
get_variable() (fsl.utils.filetree.filetree.FileTree method)
getAffine() (fsl.data.image.Nifti method)
getAllLabels() (fsl.data.volumelabels.VolumeLabels method)
getAnalysisDir() (in module fsl.data.featanalysis)
(in module fsl.data.melodicanalysis)
getAnalysisName() (fsl.data.featimage.FEATImage method)
getAtlasDescription() (fsl.data.atlases.AtlasRegistry method)
(in module fsl.data.atlases)
getClusterMask() (fsl.data.featimage.FEATImage method)
getClusterMaskFile() (in module fsl.data.featanalysis)
getComponentPowerSpectra() (in module fsl.data.melodicanalysis)
getComponentPowerSpectrum() (fsl.data.melodicimage.MelodicImage method)
getComponents() (fsl.data.volumelabels.VolumeLabels method)
getComponentTimeSeries() (fsl.data.melodicimage.MelodicImage method)
(in module fsl.data.melodicanalysis)
getCOPE() (fsl.data.featimage.FEATImage method)
getCOPEFile() (in module fsl.data.featanalysis)
getData() (fsl.data.featdesign.VoxelwiseEVMixin method)
getDataFile() (fsl.data.melodicimage.MelodicImage method)
(in module fsl.data.featanalysis)
(in module fsl.data.melodicanalysis)
getDesign() (fsl.data.featdesign.FEATFSFDesign method)
(fsl.data.featimage.FEATImage method)
getDisplayLabel() (fsl.data.volumelabels.VolumeLabels method)
getDTIFitDataPrefix() (in module fsl.data.dtifit)
getEVs() (fsl.data.featdesign.FEATFSFDesign method)
getExt() (in module fsl.data.image)
(in module fsl.utils.path)
getFEATDir() (fsl.data.featimage.FEATImage method)
getFileGroup() (in module fsl.utils.path)
getFirstLevelEVs() (in module fsl.data.featdesign)
getFIRSTPrefix() (in module fsl.data.vtk)
getFTMixFile() (in module fsl.data.melodicanalysis)
getHigherLevelEVs() (in module fsl.data.featdesign)
getICFile() (in module fsl.data.melodicanalysis)
getImageWrapper() (fsl.data.image.Image method)
getLabels() (fsl.data.volumelabels.VolumeLabels method)
getMeanFile() (fsl.data.melodicimage.MelodicImage method)
(in module fsl.data.melodicanalysis)
getMelodicDir() (fsl.data.melodicimage.MelodicImage method)
getMelodicFile() (in module fsl.data.featanalysis)
getMeta() (fsl.utils.meta.Meta method)
getMixFile() (in module fsl.data.melodicanalysis)
getNumComponents() (in module fsl.data.melodicanalysis)
getOrientation() (fsl.data.image.Nifti method)
getPE() (fsl.data.featimage.FEATImage method)
getPEFile() (in module fsl.data.featanalysis)
getReportFile() (fsl.data.featimage.FEATImage method)
(fsl.data.melodicimage.MelodicImage method)
(in module fsl.data.featanalysis)
(in module fsl.data.melodicanalysis)
getResidualFile() (in module fsl.data.featanalysis)
getResiduals() (fsl.data.featimage.FEATImage method)
getTaskThread() (fsl.data.imagewrapper.ImageWrapper method)
getThresholds() (in module fsl.data.featanalysis)
getTopLevelAnalysisDir() (fsl.data.featimage.FEATImage method)
(fsl.data.melodicimage.MelodicImage method)
(in module fsl.data.featanalysis)
(in module fsl.data.melodicanalysis)
getVertexData() (fsl.data.mesh.Mesh method)
getVertexDataColourTable() (fsl.data.freesurfer.FreesurferMesh method)
getXFormCode() (fsl.data.image.Nifti method)
getZStatFile() (in module fsl.data.featanalysis)
getZStats() (fsl.data.featimage.FEATImage method)
GiftiMesh (class in fsl.data.gifti)
glIsSoftwareRenderer() (fsl.utils.platform.Platform property)
glRenderer() (fsl.utils.platform.Platform property)
glVersion() (fsl.utils.platform.Platform property)
guessType() (in module fsl.data.utils)
H
hasAtlas() (fsl.data.atlases.AtlasRegistry method)
(in module fsl.data.atlases)
hasComponent() (fsl.data.volumelabels.VolumeLabels method)
hasExt() (in module fsl.utils.path)
hasLabel() (fsl.data.volumelabels.VolumeLabels method)
hasMelodicDir() (in module fsl.data.featanalysis)
hasStats() (fsl.data.featimage.FEATImage method)
(in module fsl.data.featanalysis)
haveGui() (fsl.utils.platform.Platform property)
header() (fsl.data.image.Nifti property)
HelpFormatter (class in fsl.scripts.atlasq)
HIDE_IF_TRUE (in module fsl.wrappers.wrapperutils)
I
identifyAffine() (fsl.data.image.Nifti static method)
identifyAtlas() (in module fsl.scripts.atlasq)
IdentifyError
idle() (fsl.utils.idle.IdleLoop method)
(in module fsl.utils.idle)
IdleLoop (class in fsl.utils.idle)
idleLoop (in module fsl.utils.idle)
IdleTask (class in fsl.utils.idle)
idleWhen() (fsl.utils.idle.IdleLoop method)
(in module fsl.utils.idle)
Image (class in fsl.data.image)
image() (fsl.data.featdesign.VoxelwiseEVMixin property)
Image() (in module fsl.utils.parse_data)
ImageOut() (in module fsl.utils.parse_data)
ImageWrapper (class in fsl.data.imagewrapper)
imcp() (in module fsl.utils.imcp)
imglob() (in module fsl.scripts.imglob)
immv() (in module fsl.utils.imcp)
inBIDSDir() (in module fsl.utils.bids)
indices() (fsl.data.mesh.Mesh property)
inferType() (in module fsl.transform.x5)
info() (in module fsl.utils.fslsub)
inIdle() (fsl.utils.idle.IdleLoop method)
initialise() (in module fsl.utils.settings)
inm() (fsl.wrappers.fslmaths.fslmaths method)
inSSHSession() (fsl.utils.platform.Platform property)
Instanceify (class in fsl.utils.memoize)
intent() (fsl.data.image.Nifti property)
intlist() (in module fsl.scripts.resample_image)
invalidate() (fsl.utils.memoize.Memoize method)
InvalidLabelFileError
invert() (in module fsl.transform.affine)
inVNCSession() (fsl.utils.platform.Platform property)
invwarp() (in module fsl.wrappers.fnirt)
invxfm() (in module fsl.wrappers.flirt)
isAllEnabled() (fsl.utils.notifier.Notifier method)
isBIDSDir() (in module fsl.utils.bids)
isBIDSFile() (in module fsl.utils.bids)
iscomplex() (fsl.data.image.Image property)
isDTIFitPath() (in module fsl.data.dtifit)
isEnabled() (fsl.utils.notifier.Notifier method)
isFEATDir() (in module fsl.data.featanalysis)
isFEATImage() (in module fsl.data.featanalysis)
isFirstLevelAnalysis() (fsl.data.featimage.FEATImage method)
(in module fsl.data.featanalysis)
isMelodicDir() (in module fsl.data.melodicanalysis)
isMelodicImage() (in module fsl.data.melodicanalysis)
isNeurological() (fsl.data.image.Nifti method)
isNoisyComponent() (in module fsl.data.fixlabels)
isQueued() (fsl.utils.idle.TaskThread method)
isValidFancySliceObj() (in module fsl.data.imagewrapper)
J
job_name (fsl.utils.fslsub.SubmitParams attribute)
K
knotSpacing() (fsl.transform.nonlinear.CoefficientField property)
L
L1() (fsl.data.dtifit.DTIFitTensor method)
L2() (fsl.data.dtifit.DTIFitTensor method)
L3() (fsl.data.dtifit.DTIFitTensor method)
label() (fsl.data.atlases.LabelAtlas method)
LabelAtlas (class in fsl.data.atlases)
labelNames() (in module fsl.scripts.atlasq)
list_all_trees() (in module fsl.utils.filetree.parse)
listAtlases() (fsl.data.atlases.AtlasRegistry method)
(in module fsl.data.atlases)
(in module fsl.scripts.atlasq)
listFiles() (fsl.utils.settings.Settings method)
(in module fsl.utils.settings)
Literal (class in fsl.utils.filetree.utils)
LOAD (in module fsl.wrappers.wrapperutils)
load() (fsl.data.volumelabels.VolumeLabels method)
load_json() (fsl.utils.filetree.filetree.FileTree class method)
load_pickle() (fsl.utils.filetree.filetree.FileTree class method)
loadAtlas() (fsl.data.atlases.AtlasRegistry method)
(in module fsl.data.atlases)
loadClusterResults() (in module fsl.data.featanalysis)
loadConfoundFiles() (in module fsl.scripts.fsl_ents)
loadContrasts() (in module fsl.data.featanalysis)
loadData() (fsl.data.image.Image method)
(fsl.data.imagewrapper.ImageWrapper method)
loadDesign() (in module fsl.data.featanalysis)
loadDesignMat() (in module fsl.data.featdesign)
loadGiftiMesh() (in module fsl.data.gifti)
loadGiftiVertexData() (in module fsl.data.gifti)
loadLabelFile() (in module fsl.data.fixlabels)
loadMetadata() (in module fsl.data.image)
(in module fsl.utils.bids)
loadSeries() (in module fsl.data.dicom)
loadSettings() (in module fsl.data.featanalysis)
loadVertexData() (fsl.data.freesurfer.FreesurferMesh method)
(fsl.data.gifti.GiftiMesh method)
(fsl.data.mesh.Mesh method)
loadVertexDataFile() (in module fsl.data.freesurfer)
loadVertices() (fsl.data.freesurfer.FreesurferMesh method)
(fsl.data.gifti.GiftiMesh method)
(fsl.data.mesh.Mesh method)
loadVestLutFile() (in module fsl.data.vest)
loadVTKPolydataFile() (in module fsl.data.vtk)
logdir (fsl.utils.fslsub.SubmitParams attribute)
looksLikeImage() (in module fsl.data.image)
looksLikeTensorImage() (in module fsl.data.dtifit)
looksLikeVestLutFile() (in module fsl.data.vest)
M
mail_options (fsl.utils.fslsub.SubmitParams attribute)
main() (in module fsl.scripts.atlasq)
(in module fsl.scripts.fsl_apply_x5)
(in module fsl.scripts.fsl_convert_x5)
(in module fsl.scripts.fsl_ents)
(in module fsl.scripts.imcp)
(in module fsl.scripts.imglob)
(in module fsl.scripts.immv)
(in module fsl.scripts.resample_image)
makeWriteable() (in module fsl.data.utils)
mapIndices() (fsl.data.image.Nifti method)
mas() (fsl.wrappers.fslmaths.fslmaths method)
MaskError
maskLabel() (fsl.data.atlases.LabelAtlas method)
maskQuery() (in module fsl.scripts.atlasq)
maskValues() (fsl.data.atlases.StatisticAtlas method)
Match (class in fsl.utils.filetree.query)
match() (fsl.utils.bids.BIDSFile method)
mcflirt() (in module fsl.wrappers.flirt)
melodic() (in module fsl.wrappers.melodic)
MelodicImage (class in fsl.data.melodicimage)
Memoize (class in fsl.utils.memoize)
memoize() (in module fsl.utils.memoize)
memoizeMD5() (in module fsl.utils.memoize)
Mesh (class in fsl.data.mesh)
Mesh() (in module fsl.utils.parse_data)
Meta (class in fsl.utils.meta)
metaItems() (fsl.utils.meta.Meta method)
metaKeys() (fsl.utils.meta.Meta method)
metaValues() (fsl.utils.meta.Meta method)
MGHImage (class in fsl.data.mghimage)
mghImageFile() (fsl.data.mghimage.MGHImage property)
MIN_DCM2NIIX_VERSION (in module fsl.data.dicom)
minutes (fsl.utils.fslsub.SubmitParams attribute)
MissingVariable
modelFit() (in module fsl.data.featimage)
module
fsl
fsl.data
fsl.data.atlases
fsl.data.bitmap
fsl.data.constants
fsl.data.dicom
fsl.data.dtifit
fsl.data.featanalysis
fsl.data.featdesign
fsl.data.featimage
fsl.data.fixlabels
fsl.data.freesurfer
fsl.data.gifti
fsl.data.image
fsl.data.imagewrapper
fsl.data.melodicanalysis
fsl.data.melodicimage
fsl.data.mesh
fsl.data.mghimage
fsl.data.utils
fsl.data.vest
fsl.data.volumelabels
fsl.data.vtk
fsl.scripts
fsl.scripts.atlasq
fsl.scripts.fsl_apply_x5
fsl.scripts.fsl_convert_x5
fsl.scripts.fsl_ents
fsl.scripts.imcp
fsl.scripts.imglob
fsl.scripts.immv
fsl.scripts.resample_image
fsl.transform
fsl.transform.affine
fsl.transform.flirt
fsl.transform.fnirt
fsl.transform.nonlinear
fsl.transform.x5
fsl.utils
fsl.utils.assertions
fsl.utils.bids
fsl.utils.cache
fsl.utils.deprecated
fsl.utils.ensure
fsl.utils.filetree
fsl.utils.filetree.filetree
fsl.utils.filetree.parse
fsl.utils.filetree.query
fsl.utils.filetree.utils
fsl.utils.fslsub
fsl.utils.idle
fsl.utils.image
fsl.utils.image.resample
fsl.utils.image.roi
fsl.utils.imcp
fsl.utils.memoize
fsl.utils.meta
fsl.utils.naninfrange
fsl.utils.notifier
fsl.utils.parse_data
fsl.utils.path
fsl.utils.platform
fsl.utils.run
fsl.utils.settings
fsl.utils.tempdir
fsl.utils.weakfuncref
fsl.version
fsl.wrappers
fsl.wrappers.bet
fsl.wrappers.eddy
fsl.wrappers.fast
fsl.wrappers.flirt
fsl.wrappers.fnirt
fsl.wrappers.fsl_anat
fsl.wrappers.fslmaths
fsl.wrappers.fugue
fsl.wrappers.melodic
fsl.wrappers.misc
fsl.wrappers.wrapperutils
MotionParameterEV (class in fsl.data.featdesign)
mul() (fsl.wrappers.fslmaths.fslmaths method)
multi_threaded (fsl.utils.fslsub.SubmitParams attribute)
mutex() (in module fsl.utils.idle)
MutexFactory (class in fsl.utils.idle)
N
name() (fsl.data.bitmap.Bitmap property)
(fsl.data.mesh.Mesh property)
(fsl.utils.filetree.filetree.FileTree property)
namedPositionals() (in module fsl.wrappers.wrapperutils)
naninfrange() (in module fsl.utils.naninfrange)
ndim() (fsl.data.image.Nifti property)
nearestVertex() (fsl.data.mesh.Mesh method)
needsFixing() (in module fsl.data.mesh)
neverQueue() (fsl.utils.idle.IdleLoop property)
nibImage() (fsl.data.image.Image property)
Nifti (class in fsl.data.image)
NIFTI_XFORM_ALIGNED_ANAT (in module fsl.data.constants)
NIFTI_XFORM_ANALYZE (in module fsl.data.constants)
NIFTI_XFORM_MNI_152 (in module fsl.data.constants)
NIFTI_XFORM_SCANNER_ANAT (in module fsl.data.constants)
NIFTI_XFORM_TALAIRACH (in module fsl.data.constants)
NIFTI_XFORM_UNKNOWN (in module fsl.data.constants)
niftiVersion() (fsl.data.image.Nifti property)
NonLinearTransform (class in fsl.transform.nonlinear)
NormalEV (class in fsl.data.featdesign)
normalise() (in module fsl.transform.affine)
normals() (fsl.data.mesh.Mesh property)
Notifier (class in fsl.utils.notifier)
notify() (fsl.utils.notifier.Notifier method)
numComponents() (fsl.data.melodicimage.MelodicImage method)
(fsl.data.volumelabels.VolumeLabels method)
numContrasts() (fsl.data.featimage.FEATImage method)
numEVs() (fsl.data.featimage.FEATImage method)
numPoints() (fsl.data.featimage.FEATImage method)
nvals() (fsl.data.image.Image property)
nvertices() (fsl.data.mesh.Mesh property)
O
ohi() (in module fsl.scripts.atlasq)
on_disk() (fsl.utils.filetree.filetree.FileTree method)
Optional (class in fsl.utils.filetree.utils)
optional_subsets() (fsl.utils.filetree.utils.Template method)
optional_variables() (fsl.utils.filetree.utils.Optional method)
(fsl.utils.filetree.utils.Part method)
(fsl.utils.filetree.utils.Template method)
(in module fsl.utils.filetree.utils)
ordered_variables() (fsl.utils.filetree.utils.Template method)
ORIENT_A2P (in module fsl.data.constants)
ORIENT_I2S (in module fsl.data.constants)
ORIENT_L2R (in module fsl.data.constants)
ORIENT_P2A (in module fsl.data.constants)
ORIENT_R2L (in module fsl.data.constants)
ORIENT_S2I (in module fsl.data.constants)
ORIENT_UNKNOWN (in module fsl.data.constants)
os() (fsl.utils.platform.Platform property)
output() (in module fsl.utils.fslsub)
OVERLAP_ALL (in module fsl.data.imagewrapper)
OVERLAP_NONE (in module fsl.data.imagewrapper)
OVERLAP_SOME (in module fsl.data.imagewrapper)
P
parent() (fsl.utils.filetree.filetree.FileTree property)
parse() (fsl.utils.filetree.utils.Template class method)
parseArgs() (in module fsl.scripts.atlasq)
(in module fsl.scripts.fsl_apply_x5)
(in module fsl.scripts.fsl_convert_x5)
(in module fsl.scripts.fsl_ents)
(in module fsl.scripts.resample_image)
parseFilename() (in module fsl.utils.bids)
parseVersionString() (in module fsl.version)
Part (class in fsl.utils.filetree.utils)
partial_fill() (fsl.utils.filetree.filetree.FileTree method)
partialFit() (fsl.data.featimage.FEATImage method)
patchVersion() (in module fsl.version)
PathError
,
[1]
pixdim() (fsl.data.image.Nifti property)
planeIntersection() (fsl.data.mesh.Mesh method)
Platform (class in fsl.utils.platform)
platform (in module fsl.utils.platform)
prelude() (in module fsl.wrappers.fugue)
prepareArgs() (in module fsl.utils.run)
prepareGiftiVertexData() (in module fsl.data.gifti)
prepareMask() (fsl.data.atlases.Atlas method)
printColumns() (in module fsl.scripts.atlasq)
priority (fsl.utils.fslsub.SubmitParams attribute)
ProbabilisticAtlas (class in fsl.data.atlases)
put() (fsl.utils.cache.Cache method)
Q
query() (fsl.utils.filetree.query.FileTreeQuery method)
queryAtlas() (in module fsl.scripts.atlasq)
queryLongOutput() (in module fsl.scripts.atlasq)
queryShortOutput() (in module fsl.scripts.atlasq)
queue (fsl.utils.fslsub.SubmitParams attribute)
queue() (fsl.utils.idle.IdleLoop property)
queueDict() (fsl.utils.idle.IdleLoop property)
R
ram (fsl.utils.fslsub.SubmitParams attribute)
rayIntersection() (fsl.data.mesh.Mesh method)
read() (fsl.utils.filetree.filetree.FileTree class method)
(fsl.utils.settings.Settings method)
(in module fsl.utils.settings)
read_line() (in module fsl.utils.filetree.parse)
read_subtree_line() (in module fsl.utils.filetree.parse)
readAll() (fsl.utils.settings.Settings method)
(in module fsl.utils.settings)
readFile() (fsl.utils.settings.Settings method)
(in module fsl.utils.settings)
readFlirt() (in module fsl.transform.flirt)
readFnirt() (in module fsl.transform.fnirt)
readLinearX5() (in module fsl.transform.x5)
readNonLinearX5() (in module fsl.transform.x5)
recip() (fsl.wrappers.fslmaths.fslmaths method)
ref() (fsl.transform.nonlinear.NonLinearTransform property)
refSpace() (fsl.transform.nonlinear.NonLinearTransform property)
refToFieldMat() (fsl.transform.nonlinear.CoefficientField property)
refToSrcMat() (fsl.transform.nonlinear.CoefficientField property)
register() (fsl.utils.notifier.Notifier method)
register_tree() (in module fsl.utils.filetree.filetree)
Registered
registered() (fsl.utils.idle.IdleLoop property)
relatedFiles() (in module fsl.data.gifti)
relatedGeometryFiles() (in module fsl.data.freesurfer)
relatedVertexDataFiles() (in module fsl.data.freesurfer)
relative() (fsl.transform.nonlinear.DeformationField property)
rem() (fsl.wrappers.fslmaths.fslmaths method)
remove_optionals() (fsl.utils.filetree.utils.Template method)
removeAtlas() (fsl.data.atlases.AtlasRegistry method)
(in module fsl.data.atlases)
removeComponent() (fsl.data.volumelabels.VolumeLabels method)
removeDuplicates() (in module fsl.utils.path)
removeExt() (in module fsl.data.image)
(in module fsl.utils.path)
removeLabel() (fsl.data.volumelabels.VolumeLabels method)
Required (class in fsl.utils.filetree.utils)
required_variables() (fsl.utils.filetree.utils.Part method)
(fsl.utils.filetree.utils.Required method)
(fsl.utils.filetree.utils.Template method)
resample() (in module fsl.utils.image.resample)
resampleToPixdims() (in module fsl.utils.image.resample)
resampleToReference() (in module fsl.utils.image.resample)
rescale() (in module fsl.transform.affine)
rescanAtlases() (fsl.data.atlases.AtlasRegistry method)
(in module fsl.data.atlases)
reset() (fsl.data.imagewrapper.ImageWrapper method)
(fsl.utils.idle.IdleLoop method)
resetWarningCache() (in module fsl.utils.deprecated)
resolve() (fsl.utils.filetree.utils.Template method)
(in module fsl.utils.filetree.utils)
rmsdev() (in module fsl.transform.affine)
robustfov() (in module fsl.wrappers.bet)
roi() (in module fsl.utils.image.roi)
rotMatToAffine() (in module fsl.transform.affine)
rotMatToAxisAngles() (in module fsl.transform.affine)
run() (fsl.utils.idle.TaskThread method)
(fsl.wrappers.fslmaths.fslmaths method)
(in module fsl.utils.idle)
(in module fsl.utils.run)
runfsl() (in module fsl.utils.run)
S
sameSpace() (fsl.data.image.Nifti method)
sanitiseList() (in module fsl.scripts.resample_image)
save() (fsl.data.image.Image method)
(fsl.data.mghimage.MGHImage method)
(fsl.data.volumelabels.VolumeLabels method)
save_json() (fsl.utils.filetree.filetree.FileTree method)
save_pickle() (fsl.utils.filetree.filetree.FileTree method)
saveLabelFile() (in module fsl.data.fixlabels)
saveState() (fsl.data.image.Image property)
scaledVoxToVoxMat() (fsl.data.image.Nifti property)
scaleOffsetXform() (in module fsl.transform.affine)
scan() (in module fsl.utils.filetree.query)
scanDir() (in module fsl.data.dicom)
search_tree() (in module fsl.utils.filetree.parse)
selectedVertices() (fsl.data.mesh.Mesh method)
seriesCRC() (in module fsl.data.dicom)
set() (in module fsl.utils.settings)
setMeta() (fsl.utils.meta.Meta method)
Settings (class in fsl.utils.settings)
sformToFlirtMatrix() (in module fsl.transform.flirt)
shallowest() (in module fsl.utils.path)
shape() (fsl.data.bitmap.Bitmap property)
(fsl.data.image.Nifti property)
(fsl.data.imagewrapper.ImageWrapper property)
SHOW_IF_TRUE (in module fsl.wrappers.wrapperutils)
sigloss() (in module fsl.wrappers.fugue)
skip() (fsl.utils.notifier.Notifier method)
skipAll() (fsl.utils.notifier.Notifier method)
skipUnchanged() (in module fsl.utils.memoize)
sliceCovered() (in module fsl.data.imagewrapper)
sliceObjToSliceTuple() (in module fsl.data.imagewrapper)
sliceOverlap() (in module fsl.data.imagewrapper)
slicer() (in module fsl.wrappers.misc)
sliceTupleToSliceObj() (in module fsl.data.imagewrapper)
splitExt() (in module fsl.data.image)
(in module fsl.utils.path)
src() (fsl.transform.nonlinear.NonLinearTransform property)
srcSpace() (fsl.transform.nonlinear.NonLinearTransform property)
srcToRefMat() (fsl.transform.nonlinear.CoefficientField property)
StatisticAtlas (class in fsl.data.atlases)
stdout() (fsl.wrappers.wrapperutils.FileOrThing.Results property)
stop() (fsl.utils.idle.TaskThread method)
strval() (fsl.data.image.Nifti method)
sub() (fsl.wrappers.fslmaths.fslmaths method)
submit() (in module fsl.utils.fslsub)
SubmitParams (class in fsl.utils.fslsub)
summariseAtlas() (in module fsl.scripts.atlasq)
surfToVoxMat() (fsl.data.mghimage.MGHImage property)
surfToWorldMat() (fsl.data.mghimage.MGHImage property)
synchronous() (fsl.utils.idle.IdleLoop method)
T
Task (class in fsl.utils.idle)
TaskThread (class in fsl.utils.idle)
TaskThreadVeto
tempdir() (in module fsl.utils.tempdir)
Template (class in fsl.utils.filetree.utils)
template() (fsl.utils.filetree.query.Match property)
template_variables() (fsl.utils.filetree.filetree.FileTree method)
templates() (fsl.utils.filetree.query.FileTreeQuery property)
TemporalDerivativeEV (class in fsl.data.featdesign)
tensorToComponents() (in module fsl.data.dtifit)
tensorToEigendecomposition() (in module fsl.data.dtifit)
thr() (fsl.wrappers.fslmaths.fslmaths method)
thresholds() (fsl.data.featimage.FEATImage method)
timer() (fsl.utils.idle.IdleLoop property)
timeUnits() (fsl.data.image.Nifti property)
Tmax() (fsl.wrappers.fslmaths.fslmaths method)
Tmean() (fsl.wrappers.fslmaths.fslmaths method)
Tmin() (fsl.wrappers.fslmaths.fslmaths method)
toFlirt() (in module fsl.transform.flirt)
toFnirt() (in module fsl.transform.fnirt)
topup() (in module fsl.wrappers.eddy)
tr() (fsl.data.melodicimage.MelodicImage property)
transform() (fsl.transform.nonlinear.CoefficientField method)
(fsl.transform.nonlinear.DeformationField method)
(fsl.transform.nonlinear.NonLinearTransform method)
(in module fsl.transform.affine)
transformNormal() (in module fsl.transform.affine)
tree() (fsl.utils.filetree.query.FileTreeQuery property)
(fsl.utils.filetree.query.Match property)
trimesh() (fsl.data.mesh.Mesh property)
Tstd() (fsl.wrappers.fslmaths.fslmaths method)
U
uniquePrefix() (in module fsl.utils.path)
update() (fsl.utils.filetree.filetree.FileTree method)
(fsl.utils.fslsub.SubmitParams method)
updateMeta() (fsl.utils.meta.Meta method)
use() (in module fsl.utils.settings)
uthr() (fsl.wrappers.fslmaths.fslmaths method)
V
V1() (fsl.data.dtifit.DTIFitTensor method)
V2() (fsl.data.dtifit.DTIFitTensor method)
V3() (fsl.data.dtifit.DTIFitTensor method)
values() (fsl.data.atlases.StatisticAtlas method)
variables() (fsl.utils.filetree.query.FileTreeQuery method)
(fsl.utils.filetree.query.Match property)
veclength() (in module fsl.transform.affine)
verbose (fsl.utils.fslsub.SubmitParams attribute)
VERTEX_ANNOT_FILES (in module fsl.data.freesurfer)
VERTEX_DATA_EXTENSIONS (in module fsl.data.gifti)
VERTEX_DATA_FILES (in module fsl.data.freesurfer)
VERTEX_LABEL_FILES (in module fsl.data.freesurfer)
VERTEX_MGH_FILES (in module fsl.data.freesurfer)
vertexDataSets() (fsl.data.mesh.Mesh method)
vertexSets() (fsl.data.mesh.Mesh method)
vertices() (fsl.data.mesh.Mesh property)
vnormals() (fsl.data.mesh.Mesh property)
VolumeLabels (class in fsl.data.volumelabels)
VoxelwiseConfoundEV (class in fsl.data.featdesign)
VoxelwiseEV (class in fsl.data.featdesign)
VoxelwiseEVMixin (class in fsl.data.featdesign)
voxToScaledVoxMat() (fsl.data.image.Nifti property)
voxToSurfMat() (fsl.data.mghimage.MGHImage property)
(in module fsl.data.mghimage)
voxToWorldMat() (fsl.data.image.Image property)
(fsl.data.image.Nifti property)
VTKMesh (class in fsl.data.vtk)
W
wait() (in module fsl.utils.fslsub)
(in module fsl.utils.idle)
(in module fsl.utils.run)
wait_for (fsl.utils.fslsub.SubmitParams attribute)
waitUntilIdle() (fsl.utils.idle.TaskThread method)
warn() (in module fsl.utils.deprecated)
WeakFunctionRef (class in fsl.utils.weakfuncref)
worldToSurfMat() (fsl.data.mghimage.MGHImage property)
worldToVoxMat() (fsl.data.image.Nifti property)
write() (fsl.utils.settings.Settings method)
(in module fsl.utils.settings)
writeConfigFile() (fsl.utils.settings.Settings method)
writeFile() (fsl.utils.settings.Settings method)
(in module fsl.utils.settings)
writeFlirt() (in module fsl.transform.flirt)
writeLinearX5() (in module fsl.transform.x5)
writeNonLinearX5() (in module fsl.transform.x5)
WX_GTK (in module fsl.utils.platform)
WX_MAC_CARBON (in module fsl.utils.platform)
WX_MAC_COCOA (in module fsl.utils.platform)
WX_PHOENIX (in module fsl.utils.platform)
WX_PYTHON (in module fsl.utils.platform)
WX_UNKNOWN (in module fsl.utils.platform)
wxFlavour() (fsl.utils.platform.Platform property)
wxPlatform() (fsl.utils.platform.Platform property)
X
X5Error
X5ToFlirt() (in module fsl.scripts.fsl_convert_x5)
X5ToFnirt() (in module fsl.scripts.fsl_convert_x5)
xyzUnits() (fsl.data.image.Nifti property)