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Merge pull request #29 from astewartau/master
Added TODO list to README.md
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README.md

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@@ -43,11 +43,11 @@ on additional functions from nipype (including `list_outputs`), each interface c
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it is set as `callable` in metadata (e.g. [here](https://github.com/nipype/pydra-fsl/blob/ceae758f76bde81465e86cff029b40e334a7939a/pydra/tasks/fsl/preprocess/fast.py#L237))
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- tests_inputs, tests_outputs: specification for tests,
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the fields should have the same length and each element should contain
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the input fields values and list of the expected output fields names
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the fields should have the same length and each element should contain
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the input fields values and list of the expected output fields names
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- doctests: specification for doctest,
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should include values for input fields and the expected `cmdline`
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should include values for input fields and the expected `cmdline`
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- python file with functions used as callables to gather the outputs:
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`specs/callables.py` should contain all the functions from `output_callables`;
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Tests can be run using `pytest`:
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pytest -vs pydra/tasks/fsl/{module_name}/tests
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## Interface progress
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Below is a list of all planned interfaces, with completed interfaces checked. The list was copied from the nipype documentation at https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.fsl.html.
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### Preprocess
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- [x] ApplyWarp (`applywarp`)
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- [ ] ApplyXFM (`flirt`)
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- [x] BET (`bet`)
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- [x] FAST (`fast`)
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- [x] FIRST (`first`)
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- [x] FLIRT (`flirt`)
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- [x] FNIRT (`fnirt`)
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- [ ] FUGUE (`fugue`)
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- [x] MCFLIRT (`mcflirt`)
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- [x] PRELUDE (`prelude`)
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- [x] SUSAN (`susan`)
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- [x] SliceTimer (`slicetimer`)
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### AROMA
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- [ ] ICA_AROMA (`ICA_AROMA.py`)
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### DTI
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- [ ] BEDPOSTX / BEDPOSTX5 (`bedpostx`)
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- [ ] DTIFit (`dtifit`)
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- [ ] DistanceMap (`distancemap`)
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- [ ] FSLXCommand (`xfibres` and `bedpost`)
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- [ ] FindTheBiggest (`find_the_biggest`)
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- [ ] MakeDyadicVectors (`make_dyadic_vectors`)
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- [ ] ProbTrackX (`probtrackx`)
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- [ ] ProbTrackX2 (`probtrackx2`)
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- [ ] ProjThresh (`proj_thresh`)
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- [ ] TractSkeleton (`tbss_skeleton`)
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- [ ] VecReg (`vecreg`)
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- [ ] XFibres / XFibres5 (`xfibres`)
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## EPI
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- [ ] ApplyTOPUP (`applytopup`)
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- [ ] EPIDeWarp (`epidewarp.fsl`; depreciated)
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- [ ] Eddy (`eddy_openmp`)
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- [ ] EddyCorrect (`eddy_correct`; depreciated)
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- [ ] EddyQuad (`eddy_quad`)
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- [ ] EpiReg (`epi_reg`)
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- [ ] PrepareFieldmap (`fsl_prepare_fieldmap`)
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- [ ] SigLoss (`sigloss`)
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- [ ] TOPUP (`topup`)
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## FIX
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- [ ] Classifier (`fix -c`)
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- [ ] Cleaner (`fix -a`)
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- [ ] FeatureExtractor (`fix -f`)
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- [ ] Training (`fix -t`)
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- [ ] TrainingSetCreator
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## Utils
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- [ ] AvScale (`avscale`)
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- [ ] Complex (`fslcomplex`)
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- [ ] ConvertWarp (`convertwarp`)
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- [ ] ConvertXFM (`convert_xfm`)
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- [ ] CopyGeom (`fslcpgeom`)
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- [ ] ExtractROI (`fslroi`)
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- [ ] FilterRegressor (`fsl_regfilt`)
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- [ ] ImageMaths (`fslmaths`)
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- [ ] ImageMeants (`fslmeants`)
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- [ ] ImageStats (`fslstats`)
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- [ ] InvWarp (`invwarp`)
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- [ ] Merge (`fslmerge`)
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- [ ] MotionOutliers (`fsl_motion_outliers`)
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- [ ] Overlay (`overlay`)
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- [ ] PlotMotionParams (`fsl_tsplot`)
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- [ ] PlotTimeSeries (`fsl_tsplot`)
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- [ ] PowerSpectrum (`fslpspec`)
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- [ ] Reorient2Std (`fslreorient2std`)
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- [ ] RobustFOV (`robustfov`)
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- [ ] SigLoss (`sigloss`)
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- [ ] Slice (`fslslice`)
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- [ ] Slicer (`slicer`)
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- [ ] Smooth (`fslmaths`)
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- [ ] Split (`fslsplit`)
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- [ ] SwapDimensions (`fslswapdim`)
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- [ ] Text2Vest (`text2vest`)
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- [ ] Vest2Text (`vest2text`)
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- [ ] WarpPoints (`img2imgcoord`)
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- [ ] WarpPointsFromStd (`std2imgcoord`)
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- [ ] WarpPointsToStd (`img2stdcoord`)
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- [ ] WarpUtils (`fnirtfileutils`)
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### POSSUM
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- [ ] B0Calc (`b0calc`)
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### Model
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- [ ] Cluster (`cluster`)
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- [ ] ContrastMgr (`contrast_mgr`)
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- [ ] DualRegression (`dual_regression`)
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- [ ] FEAT (`feat`)
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- [ ] FEATModel (`feat_model`)
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- [ ] FEATRegister
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- [ ] FILMGLS (`film_gls`)
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- [ ] FLAMEO (`flameo`)
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- [ ] GLM (`fsl_glm`)
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- [ ] L2Model
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- [ ] Level1Design
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- [ ] MELODIC (`melodic`)
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- [ ] MultipleRegressDesign
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- [ ] Randomise (`randomise`)
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- [ ] SMM (`mm --ld=logdir`)
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- [ ] SmoothEstimate (`smoothest`)
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### Maths
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- [ ] AR1Image (`fslmaths`)
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- [ ] ApplyMask (`fslmaths`)
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- [ ] BinaryMaths (`fslmaths`)
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- [ ] ChangeDataType (`fslmaths`)
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- [ ] DilateImage (`fslmaths`)
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- [ ] ErodeImage (`fslmaths`)
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- [ ] IsotropicSmooth (`fslmaths`)
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- [ ] MathsCommand (`fslmaths`)
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- [ ] MaxImage (`fslmaths`)
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- [ ] MaxnImage (`fslmaths`)
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- [ ] MeanImage (`fslmaths`)
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- [ ] MedianImage (`fslmaths`)
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- [ ] MinImage (`fslmaths`)
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- [ ] MultiImageMaths (`fslmaths`)
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- [ ] PercentileImage (`fslmaths`)
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- [ ] SpatialFilter (`fslmaths`)
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- [ ] StdImage (`fslmaths`)
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- [ ] TemporalFilter (`fslmaths`)
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- [ ] Threshold (`fslmaths`)
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- [ ] UnaryMaths (`fslmaths`)

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