bidspm
Content
bidspm
Installation
From docker hub
From the source
Installing the Command line Interface (CLI)
BIDS validation
BIDS stats model validation
BIDS dataset validation
Usage
Creating a default BIDS statistical model
GLM
Preprocessing
Features
Statistics
Preprocessing
Quality control:
Citation
Posters
Contributors
Installation
Dependencies
Octave compatibility
Installation
Initialization
Installation on a computing cluster
Usage notes
API
Command line API
Positional Arguments
Named Arguments
preprocess only arguments
create roi only arguments
stats only arguments
Configuration
Options
Defaults
spm_my_defaults
statistics defaults
Serial correlation modelisation
SPM to BIDS filename conversion
Setting directories
List of defaults
BIDS stats model
Validate your model
In Visual Studio Code
In the browser
Using the BIDS stats model python package
Loading and interacting with a BIDS stats model
bidspm implementation of the BIDS stats model
Transformation
HRF
Software
Results
Contrasts
Run level
Subject level
Dataset level
Method section
Parametric modulation
Examples
Demos
MoAE
Face repetition
Visual motion localizers
Using bidspm and datalad
Set up
Running the analysis
Openneuro based demos
Demos based on openneuro datasets
Download with datalad
NARPS: ds001734
Statistics
Statistics workflows
Subject level
Compute results
Preprocessing
Preprocessing workflows
Slice Time Correction
Spatial Preprocessing
Smoothing
Others
Outputs of bidspm
jobs and logs
preprocessing
func
anat
Statistics
Mapping
Methods section
Dataset description
Preprocessing & GLM
Output example - Preprocessing
Pre processing
References
Output example - GLM subject level
fMRI statistical analysis
References
Output example - GLM Group level
Frequently Asked Questions
BIDS: What is a BIDS way to name and store Regions of Interest (ROIs)?
General: Can I use parallelization with bidspm?
General: How can I know that things are set up properly before I run an analysis?
General: How can I prevent from having SPM windows pop up all the time?
General: How can I run bidspm from the command line?
General: How can I run bidspm only certain files, like just the session
02
for example?
bids
filter
file
opt.query
General: What happens if we run same code twice?
Results: How can I change which slices are shown in a montage?
SPM: How can get the data from some specific voxel in a nifti image?
spm_read_vols
spm_get_data
SPM: How can I use SPM image calculator (
imcalc
) to create a ROI?
SPM: How can set the value of a specific voxel in a nifti image?
SPM: How do I get the header of a nifti image?
Getting the header
Voxel size
Getting the voxel subscripts of a given set of world space coordinates
Getting the world space coordinate of a given voxel
SPM: How do I know which matlab function performs a given SPM process?
SPM: How do I merge 2 masks with SPM?
SPM: What is the content of the SPM.mat file?
details on experiment
basis function
Session structure
user-specified covariates/regressors
conditions & modulators specified
parameters/modulators specified
scan indices for sessions
effect indices for sessions
F Contrast information for input-specific effects
global variate/normalization details
design matrix information
header info
structure describing intrinsic temporal non-sphericity
filtering information
masking information
design information
details on scanner data
info on beta files
info on variance of the error
info on mask
contrast details
Statistics: How can change the name of the folder of the subject level analysis?
Statistics: How can I see what the transformation in the BIDS stats model will do to my events.tsv?
Statistics: How should I name my conditions in my events.tsv?
Statistics: How should I structure my data to run my statistical analysis?
Fieldmaps
Quality control
Manual coregistration
Docker
Get image from docker hub
Build the docker image locally
Run the docker image
Changelog
[Unreleased]
Added
Changed
Deprecated
Removed
Fixed
Security
[3.1.0] - 2023-07-01
Added
Changed
Removed
Fixed
[3.0.0] - 2022-12-14
Changed
Added
Fixed
[2.3.0] - 2022-11-22
Added
Fixed
[2.2.0] - 2022-10-29
Added
Changed
Fixed
[2.1.0] - 2022-07-21
Added
Changed
Fixed
[2.0.0] - 2022-07-10
Added
Changed
Fixed
Links and references
SPM starters
Andrew Jahn videos and blogs
SPM code snippets
Bilbiography
Contributing guidelines
Installation
Initialisation
Style guidelines
Input arguments ordering
Output arguments ordering
Exceptions
Updating the FAQ
release protocol
Developers documentation
workflows
workflows roi
workflows lesion
workflows stats
workflows preproc
batches
batches lesion
batches stats
batches preproc
IO
QA
bids
bids_model
cli
constants
defaults
infra
messages
preproc fieldmaps
preproc utils
reports
stats results
stats subject_level
stats group_level
stats utils
utils
validators
bidspm
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
A
addConfoundsToDesignMatrix() (built-in function)
addGitIgnore() (built-in function)
addLicense() (built-in function)
addReadme() (built-in function)
addStcToQuery() (built-in function)
ALI_my_defaults() (built-in function)
allRunsHaveSameNbRegressors() (built-in function)
anatQA() (built-in function)
appendContrast() (built-in function)
B
baseInputParser() (built-in function)
bidsChangeSuffix() (built-in function)
bidsCheckVoxelSize() (built-in function)
bidsConcatBetaTmaps() (built-in function)
bidsCopyInputFolder() (built-in function)
bidsCreateROI() (built-in function)
bidsCreateVDM() (built-in function)
bidsFFX() (built-in function)
bidsGenerateT1map() (built-in function)
bidsInverseNormalize() (built-in function)
bidsLesionAbnormalitiesDetection() (built-in function)
bidsLesionOverlapMap() (built-in function)
bidsLesionSegmentation() (built-in function)
BidsModel (built-in class)
bidsModelSelection() (built-in function)
bidspmHelp() (built-in function)
bidsQApreproc() (built-in function)
bidsRealignReslice() (built-in function)
bidsRealignUnwarp() (built-in function)
bidsRemoveDummies() (built-in function)
bidsRename() (built-in function)
bidsReport() (built-in function)
bidsResliceTpmToFunc() (built-in function)
bidsResults() (built-in function)
bidsRFX() (built-in function)
bidsRoiBasedGLM() (built-in function)
bidsSegmentSkullStrip() (built-in function)
bidsSmoothContrasts() (built-in function)
bidsSmoothing() (built-in function)
bidsSpatialPrepro() (built-in function)
bidsSTC() (built-in function)
bidsWholeBrainFuncMask() (built-in function)
boilerplate() (built-in function)
bugReport() (built-in function)
buildIndividualSpaceRoiFilename() (built-in function)
C
censoring() (built-in function)
checkColumnParticipantsTsv() (built-in function)
checkContrast() (built-in function)
checkDependencies() (built-in function)
checkFmriprep() (built-in function)
checkGroupBy() (built-in function)
checkMaskOrUnderlay() (built-in function)
checkOptions() (built-in function)
checkRegressorName() (built-in function)
checkToolbox() (built-in function)
cleanCrash() (built-in function)
cleanUpWorkflow() (built-in function)
cliBayesModel() (built-in function)
cliCopy() (built-in function)
cliCreateRoi() (built-in function)
cliDefaultModel() (built-in function)
cliPreprocess() (built-in function)
cliSmooth() (built-in function)
cliStats() (built-in function)
compileScrubbingStats() (built-in function)
computeCumulativeFwhm() (built-in function)
computeDesignEfficiency() (built-in function)
computeFDandRMS() (built-in function)
computeMeanValueInMask() (built-in function)
computeRobustOutliers() (built-in function)
computeTsnr() (built-in function)
constructContrastNameFromBidsEntity() (built-in function)
convertOnsetTsvToMat() (built-in function)
convertPvalueToString() (built-in function)
convertRealignParamToTsv() (built-in function)
copyFigures() (built-in function)
copyGraphWindownOutput() (built-in function)
createAndReturnCounfoundMatFile() (built-in function)
createAndReturnOnsetFile() (built-in function)
createConfounds() (built-in function)
createDataDictionary() (built-in function)
createDefaultStatsModel() (built-in function)
createDerivativeDir() (built-in function)
createGlmDirName() (built-in function)
createModelFamilies() (built-in function)
createPialSurface() (built-in function)
D
defaultContrastsStructure() (built-in function)
defaultResultsStructure() (built-in function)
deleteResidualImages() (built-in function)
demos.face_repetition (module)
demos.MoAE (module)
deprecated() (built-in function)
deregexify() (built-in function)
designMatrixFigureName() (built-in function)
displayArguments() (built-in function)
E
elapsedTime() (built-in function)
errorHandling() (built-in function)
F
fileFilterForBold() (built-in function)
fillInResultStructure() (built-in function)
findSubjectConImage() (built-in function)
G
generatedBy() (built-in function)
getAcquisitionTime() (built-in function)
getAnatFilename() (built-in function)
getAndCheckRepetitionTime() (built-in function)
getAndCheckSliceOrder() (built-in function)
getBidsFilterFile() (built-in function)
getBlipDirection() (built-in function)
getBoldFilename() (built-in function)
getBoldFilenameForFFX() (built-in function)
getConfoundsRegressorFilename() (built-in function)
getContrastNb() (built-in function)
getContrastsFromParentNode() (built-in function)
getContrastsList() (built-in function)
getContrastsListForFactorialDesign() (built-in function)
getData() (built-in function)
getDist2surf() (built-in function)
getDummyContrastFromParentNode() (built-in function)
getDummyContrastsList() (built-in function)
getEnvInfo() (built-in function)
getEventsData() (built-in function)
getEventSpecificationRoiGlm() (built-in function)
getFFXdir() (built-in function)
getFuncVoxelDims() (built-in function)
getHRFderivatives() (BidsModel method)
getInclusiveMask() (built-in function)
getInclusiveMaskThreshold() (BidsModel method)
getInfo() (built-in function)
getMeanFuncFilename() (built-in function)
getMetadataFromIntendedForFunc() (built-in function)
getModelMask() (BidsModel method)
getOptionsFromCliArgument() (built-in function)
getOptionsFromModel() (built-in function)
getRegressorIdx() (built-in function)
getRepoInfo() (built-in function)
getRFXdir() (built-in function)
getROIs() (built-in function)
getSerialCorrelationCorrection() (BidsModel method)
getSessionForRegressorNb() (built-in function)
getSubjectList() (built-in function)
getTotalReadoutTime() (built-in function)
getTpmFilename() (built-in function)
getVdmFile() (built-in function)
getVersion() (built-in function)
groupLevelGlmType() (built-in function)
I
initBids() (built-in function)
inputParserForBayesModel() (built-in function)
inputParserForCopy() (built-in function)
inputParserForCreateModel() (built-in function)
inputParserForCreateRoi() (built-in function)
inputParserForPreprocess() (built-in function)
inputParserForSmooth() (built-in function)
inputParserForStats() (built-in function)
isMni() (built-in function)
isSkullstripped() (built-in function)
isTtest() (built-in function)
isZipped() (built-in function)
L
labelActivations() (built-in function)
labelSpmSessWithBidsSesAndRun() (built-in function)
lib.mancoreg (module)
loadAndCheckOptions() (built-in function)
logger() (built-in function)
lowLevelActions() (built-in function)
M
MACS_my_defaults() (built-in function)
mancoreg() (built-in function)
mancoregCallbacks() (built-in function)
mniToIxi() (built-in function)
mriqcQA() (built-in function)
N
newContrast() (built-in function)
noRoiFound() (built-in function)
noSPMmat() (built-in function)
notImplemented() (built-in function)
O
onsetsMatToTsv() (built-in function)
orderAndPadCounfoundMatFile() (built-in function)
overwriteDir() (built-in function)
P
plotConfounds() (built-in function)
plotEvents() (built-in function)
plotRoiTimeCourse() (built-in function)
printAvailableContrasts() (built-in function)
printBatchName() (built-in function)
printCredits() (built-in function)
printProcessingSubject() (built-in function)
printToScreen() (built-in function)
printWorkflowName() (built-in function)
R
realignQA() (built-in function)
regexify() (built-in function)
regressorsMatToTsv() (built-in function)
removeDummies() (built-in function)
removeEmptyQueryFields() (built-in function)
removeIntercept() (built-in function)
renameNidm() (built-in function)
renameOutputResults() (built-in function)
renamePng() (built-in function)
renamePngCsvResults() (built-in function)
renameSegmentParameter() (built-in function)
renameSpmT() (built-in function)
renameUnwarpParameter() (built-in function)
reorderCounfounds() (built-in function)
resizeAliMask() (built-in function)
returnBatchFileName() (built-in function)
returnBsmDocURL() (built-in function)
returnContrastImageFile() (built-in function)
returnDependency() (built-in function)
returnHomeDir() (built-in function)
returnName() (built-in function)
returnNameSkullstripOutput() (built-in function)
returnNumberScrubbedTimePoints() (built-in function)
returnRepoURL() (built-in function)
returnResultNameSpec() (built-in function)
returnRootDir() (built-in function)
returnRtdURL() (built-in function)
returnVolumeList() (built-in function)
roiGlmOutputName() (built-in function)
S
sanitizeConfounds() (built-in function)
saveAndRunWorkflow() (built-in function)
saveMatlabBatch() (built-in function)
saveOptions() (built-in function)
saveRoiGlmSummaryTable() (built-in function)
saveSpmScript() (built-in function)
segmentationAlreadyDone() (built-in function)
selectConfoundsByVarianceExplained() (built-in function)
set_spm_2_bids_defaults() (built-in function)
setBachRename() (built-in function)
setBatch3Dto4D() (built-in function)
setBatchComputeVDM() (built-in function)
setBatchContrasts() (built-in function)
setBatchCoregistration() (built-in function)
setBatchCoregistrationFmap() (built-in function)
setBatchCoregistrationFuncToAnat() (built-in function)
setBatchCreateVDMs() (built-in function)
setBatchEstimateModel() (built-in function)
setBatchFactorialDesign() (built-in function)
setBatchFactorialDesignImplicitMasking() (built-in function)
setBatchFatorialDesignGlobalCalcAndNorm() (built-in function)
setBatchGenerateT1map() (built-in function)
setBatchGroupLevelContrasts() (built-in function)
setBatchGroupLevelResults() (built-in function)
setBatchImageCalculation() (built-in function)
setBatchInverseNormalize() (built-in function)
setBatchLesionAbnormalitiesDetection() (built-in function)
setBatchLesionOverlapMap() (built-in function)
setBatchLesionSegmentation() (built-in function)
setBatchMeanAnatAndMask() (built-in function)
setBatchNormalizationSpatialPrepro() (built-in function)
setBatchNormalize() (built-in function)
setBatchPrintFigure() (built-in function)
setBatchRealign() (built-in function)
setBatchRenameSegmentParameter() (built-in function)
setBatchReorient() (built-in function)
setBatchReslice() (built-in function)
setBatchResults() (built-in function)
setBatchSaveCoregistrationMatrix() (built-in function)
setBatchSegmentation() (built-in function)
setBatchSelectAnat() (built-in function)
setBatchSkullStripping() (built-in function)
setBatchSmoothConImages() (built-in function)
setBatchSmoothing() (built-in function)
setBatchSmoothingAnat() (built-in function)
setBatchSmoothingFunc() (built-in function)
setBatchSTC() (built-in function)
setBatchSubjectLevelContrasts() (built-in function)
setBatchSubjectLevelGLMSpec() (built-in function)
setBatchSubjectLevelResults() (built-in function)
setBatchTwoSampleTTest() (built-in function)
setDirectories() (built-in function)
setFields() (built-in function)
setGraphicWindow() (built-in function)
setMontage() (built-in function)
setNidm() (built-in function)
setRenamingConfig() (built-in function)
setUpWorkflow() (built-in function)
silenceOctaveWarning() (built-in function)
skullstrippingAlreadyDone() (built-in function)
specifyContrasts() (built-in function)
specifyDummyContrasts() (built-in function)
specifySessionLvlContrasts() (built-in function)
specifySubLvlContrasts() (built-in function)
SPM (BidsModel attribute)
spm_my_defaults() (built-in function)
src.messages (module)
T
tempName() (built-in function)
timeStamp() (built-in function)
U
unfoldStruct() (built-in function)
unzipAndReturnsFullpathName() (built-in function)
V
validate() (built-in function)
validateConstrasts() (BidsModel method)
validateContrasts() (built-in function)
validateResultsStructure() (built-in function)
validationInputFile() (built-in function)
volumeSplicing() (built-in function)
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