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DKI Microstructural model #1226

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merged 63 commits into from
Apr 19, 2017
Merged

DKI Microstructural model #1226

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bda9272
NF: add a helper function for the kt maxima converge algorithm
RafaelNH Apr 5, 2016
752df5d
STYLE: function _directional_kurtosis should apear first than apparen…
RafaelNH Apr 5, 2016
3b33436
NF: Add function that finds kurtosis maxima and its spatial direction
RafaelNH Apr 5, 2016
1058e0c
TEST: Add a first test to access the performance of the function to f…
RafaelNH Apr 5, 2016
21f4927
TEST: Add a second test to access the performance of the function to …
RafaelNH Apr 5, 2016
36866d2
Test: Add test to access the first measure already implemented in the…
RafaelNH Apr 5, 2016
cc758bf
DOC, STYLE: Absolute imports and correction of typos
RafaelNH May 17, 2016
600ee9d
RF: defaults min kurtosis is always set to -3./7
RafaelNH May 17, 2016
4e1cb27
BF, TEST: replace kurtosis_maxima to kurtosis_maximum
RafaelNH May 17, 2016
8f00707
TEST, BF: Reduce sensitivity of ground truth maximum kurtosischeck
RafaelNH May 18, 2016
b91f89c
RF: Rename the axonal_water_fraction function name
RafaelNH May 18, 2016
950a495
NF: Complete version of diffusion_components function (test needed)
RafaelNH Jun 16, 2016
f13190f
TEST, BF: Test function diffusion_components and fix bugs
RafaelNH Jun 16, 2016
2481fe5
TEST: Add multivoxels tests for DKI's microstructural model
RafaelNH Nov 5, 2016
d863d69
RF: Add multi-voxel simulation with background voxel and improve DKI …
RafaelNH Nov 8, 2016
592f6fc
PEP8
RafaelNH Apr 11, 2017
29a0d3a
PEP8, BF: Pep8 corrections and adding functions accidentaly removed a…
RafaelNH Apr 12, 2017
2b6df80
RF, BF: Solving memory issues in diffusion_components
RafaelNH Apr 12, 2017
d92b803
RF: Add dki microstructural code in separate file dki_micro.py
RafaelNH Apr 12, 2017
c49f100
RF: removing microstructura code in dki.py
RafaelNH Apr 12, 2017
16ac9ab
RF: Adding the algorithm to find maximum kurtosis in dki.py
RafaelNH Apr 12, 2017
7a8f090
TEST: Update tests for evaluating maximum kurtosis estimates of singl…
RafaelNH Apr 12, 2017
82b5c58
RF: maxima kurtosis estimation for multivoxel data
RafaelNH Apr 13, 2017
612a2ed
DOC: Insure that functions using kmin=-3./7 have its value reference
RafaelNH Apr 13, 2017
9acdf47
RF: Re-alocate _directional_kurtosis position
RafaelNH Apr 13, 2017
7e258cd
RF: Remove code redundancy in dki_micro.py
RafaelNH Apr 13, 2017
a558652
RF: Update functions to compute awf
RafaelNH Apr 13, 2017
0a49783
TEST: Add awf and decompose tensor tests in test_dki_micro.py
RafaelNH Apr 13, 2017
a7ab6aa
NF, TEST: DKI gives error if data with only one non-zero b-value is g…
RafaelNH Apr 13, 2017
38ca395
TEST: Test maximum kurtosis finding when a mask and sphere is given
RafaelNH Apr 13, 2017
9373b4e
RF: Changing DKI fitting default from OLS to WLS
RafaelNH Apr 13, 2017
07145fb
DOC: Fix documentation of predict function of DiffusionKurtosisFit
RafaelNH Apr 13, 2017
a166342
NF: Define DKI microstructure model and fit classes
RafaelNH Apr 13, 2017
15871db
NF: Add properties into KurtosisMicrostructuralFit object
RafaelNH Apr 13, 2017
bea4edc
TEST, BF: Add DKI microstructure object tests, code bug fixed
RafaelNH Apr 13, 2017
f2fc4bb
TEST, BF: Add multi-voxel test for dki_micro objects
RafaelNH Apr 14, 2017
6599055
TEST, BF: Add prediction funtion tests and bug fix
RafaelNH Apr 14, 2017
5f146ff
RF: _directional_kurtosis to directional_kurtosis
RafaelNH Apr 14, 2017
e6627de
DOC: Correct typos in documentation
RafaelNH Apr 14, 2017
336e9e2
DOC: more typos corrected
RafaelNH Apr 14, 2017
29cd126
DOC: Further corrections of documentation, changing the following terms:
RafaelNH Apr 14, 2017
0b4b607
Split up directional kurtosis calculation into sub-functions.
arokem Apr 14, 2017
e20aa7d
RF, DOC, BF: Work on _adc and _akc. Note functions are renamed as:
RafaelNH Apr 14, 2017
711edd4
RF: Rewrite code according to directional functions. Note ALSO
RafaelNH Apr 14, 2017
3fd4fb7
DOC: document the changes done in the default max_kurtosis values
RafaelNH Apr 14, 2017
f6108d4
NF: Raise error for cases that users calls diffusion microstructural …
RafaelNH Apr 14, 2017
424d4e2
RF: Check number of b-values using function check_multi_b:
RafaelNH Apr 14, 2017
f9c7ccc
BF: Fix a bug in the radial_kurtosis function
RafaelNH Apr 14, 2017
d133e93
BF: Fix bugs in decompose_tensors:
RafaelNH Apr 15, 2017
ef84457
TEST, BF: Fix prediction tests
RafaelNH Apr 15, 2017
af25322
TEST, BF: Edit tests for prediction procedures and correct dki_micro_…
RafaelNH Apr 15, 2017
998cea3
TEST: Small adjustments in tests
RafaelNH Apr 15, 2017
e07235a
RF, BF: Fix directional_kurtosis function and simplify un-needed if...
RafaelNH Apr 18, 2017
b32f759
NF: Add more keywords in common_fit_methods
RafaelNH Apr 18, 2017
5282e9b
Un-needed 'if...else' structure shortened and simplified in dti.py
RafaelNH Apr 18, 2017
97d216f
TEST: testing the performance of kurtosis_maxima search when kurtosis…
RafaelNH Apr 18, 2017
872e844
RF, BF, DOC: More tests and bugs fixed in dki_micro.py
RafaelNH Apr 18, 2017
55a99ff
DOC: Update DKI usage example with microstructural parameter estimate…
RafaelNH Apr 18, 2017
f772340
RF: Remove min_diffusivity in tensors decomposition and tortuosity es…
RafaelNH Apr 18, 2017
1ebaddf
DOC: Correct the typos on the usage example following @arokem's comme…
RafaelNH Apr 18, 2017
cce6e1b
DOC: Correct the typos on dki.py according to @arokem's comments in PR
RafaelNH Apr 18, 2017
7717f6e
DOC: Correct the typos on dki_micro.py according to @arokem's comment…
RafaelNH Apr 18, 2017
3f401d7
TEST: Test if errors are raised when diffusion compartments are calle…
RafaelNH Apr 18, 2017
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