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  # fslfeatsetup Python functions to create an FSL FEAT configuration file (.fsf) Can be run from python command line/REPL or incorporated into a script **Alpha version available on PyPI** ```pip install fslfeatsetup``` Feel free to contribute [DOCUMENTATION](build/docs/content/api-documentation.md) generated by [pydoc-markdown](https://github.com/NiklasRosenstein/pydoc-markdown) [On Python Package Index](https://pypi.org/project/fslfeatsetup/) ## Overview The .fsf file is represented by the class `FeatSettings`, which is constructed with the analysis level and analysis type options.  Each panel of the FEAT GUI is represented by a separate class, taking the initial `FeatSettings` object as its argument. Each of these objects has a `Configure()` function taking keyword arguments specifying the options available in that panel of the GUI. These are the `MiscOptions`, `DataOptions`, `PreStatsOptions`, `RegOptions`, `StatsOptions`, and `PostStatsOptions` classes. For example the checkboxes and inputs on the Misc Options GUI panel correspond to the key-word arguments in the `MiscOptions.Configure()` function. `MiscOptions.Configure(brainThreshold=10, noiseLevel=0.66, temporalSmoothness=0.05, zThreshold=5.3, cleanupFirstLevel=False, overwriteOriginalPostStats = False, estimateNoiseFromData=False)` (*Some of these options pertain only to higher-level analyses*)  Dropdown lists are represented by enum-like classes: `PreStatsOptions.Configure(st = FeatSliceTiming.REGULAR_UP)` `PreStatsOptions.Configure(st = FeatSliceTiming.TIMING_FILE, sliceTimingFile = "path/to/file")`  ## First-level analysis example ```python from fslfeatsetup.FSF import * from fslfeatsetup.EVs import * from fslfeatsetup.FSFLabels import * SubjectFMRI = [ ... ] SubjectStructurals = [ ... ] for i in range(len(SubjectFMRI)): # initialize the FeatSettings object FSF = FeatSettings(FeatLevel.FIRST_LEVEL, FeatAnalysis.FULL_ANALYSIS) # Configure the Data options Data = DataOptions(FSF) # The only required inputs are the output FEAT directory, and the list of # FMRI files (or lower-level feats, see Higher Level Analysis example Data.Configure("path/to/output/subject_i",[SubjectFMRI[i]]) # Configure the Miscellaneous options Misc = MiscOptions(FSF) # There are NO required inputs. Using the defaults specified in my FSL installation. # If fslfeatsetup needs an option that is not in the defaults, it will let you know Misc.Configure() # Configure Registration options Reg = RegOptions(FSF) # I can specify a standard to use, or I can go with the default 2mm MNI152, as I am here Reg.ConfigureStandardSpace() # The only required argument Reg.ConfigureMainStructural([SubjectStructurals[i]]) # If I don't want to use expanded functional data, I simply don't configure it # Reg.ConfigureExpandedFunctional([ this would be a list of your expanded functional images ]) # Configure Pre-Stats options PreStats = PreStatsOptions(FSF) # The library has built-in enum-like structures that hardcode the FEAT options PreStats.Configure(sliceTiming=FeatSliceTiming.TIMING_FILE, sliceTimingFile="path/to/slice/timing/file", bet=True) # Configure Stats options Stats = StatsOptions(FSF) # using all defaults, so I don't need to specify keyword arguments Stats.Configure() # Add EVs from custom 3 column text formats. # Note that ONLY the 3-column text file format is currently supported # specify the parameters of the convolution function, or use defaults Stats.AddFirstLevelEV("myEV1","path/to/my/EV1",Gamma(phase=0, stdev=3, lag=6)) Stats.AddFirstLevelEV("myEV2","path/to/my/EV2",Gamma()) Stats.AddFirstLevelEV("myEV3","path/to/my/EV3",Gamma()) # orthogonalize # The argument is a pythonic matrix (list of lists) # the size of this matrix will be one larger than the number of EVs Stats.OrthogonalizeEVs([ [ 0 for x in range(4)] for y in range(4)]) # Configure Post-Stats options PostStats = PostStatsOptions(FSF) # using all defaults except for min and max Z-threshold for rendering PostStats.Configure(zmin = 2, zmax= 8) # write to .fsf file FSF.write("path/to/subject_i/fsf") ``` ## Higher-level analysis steps todo ## Changelog | PyPI version | Description | | ------ | ------ | | 0.3.4 | fixes related to the Issues page. No methods or classes are different | | 0.2.8 | Generated an .fsf accepted by FEAT. There are a bunch of hard-coded defaults that still need to be fixed | | 0.2.5 | Fixed gammadelay being blank and FSLDIR not found | | 0.2.3 | Patch: quotations for custom EV files | | 0.2.1 | Patched a silly bug | | 0.2.0 | first "complete" version, with post-stats options and auto generated comments. still very much a work in progress | | 0.1.2 | first stable version - package still a work in progress |