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[WIP/ENH] Add antsMotionCorr and related utilities #1812

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[WIP/ENH] Add antsMotionCorr and related utilities #1812

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8a824cb
partial implementation of an interface for antsMotionCorr. Outputs st…
rwblair Jan 27, 2017
1e17d9e
add documentation on where transformation format comes from. Added re…
rwblair Jan 27, 2017
3b0ccfa
first attempt at adding antsMotionCorrStats interface. Added more out…
rwblair Jan 27, 2017
47df181
add a gen_filename entry for output_average_image in antsMotionCorr, …
rwblair Jan 28, 2017
39d986a
fix syntax errors in ants preprocess
rwblair Jan 30, 2017
3b5f99d
get argstrs in line for ants motion correction
rwblair Feb 2, 2017
94e6504
Merge branch 'master' of github.com:nipy/nipype into add_antsMotionCorr
rwblair Feb 8, 2017
1c57878
add interface to convert ants motion correction matrices to fsl style…
rwblair Feb 14, 2017
ddaa767
Merge branch 'master' of github.com:nipy/nipype into add_antsMotionCorr
rwblair Feb 14, 2017
dc195e7
Merge branch 'master' of github.com:nipy/nipype into add_antsMotionCorr
rwblair Mar 1, 2017
06de305
fixup input spec
rwblair Mar 1, 2017
df72040
add descriptions to antsmotioncorrstats outputs
rwblair Mar 1, 2017
99c9fb5
instantiate Str trait properly
rwblair Mar 1, 2017
9bb5208
remove trailing whitespace
rwblair Mar 1, 2017
691a7b5
Update preprocess.py
oesteban Mar 1, 2017
84c397d
reorder genfilename logic
rwblair Mar 1, 2017
52a055e
resolve merge conflict
rwblair Mar 1, 2017
97b32ef
fix output_average_image decleration.
rwblair Mar 1, 2017
ff51667
remove test wat
rwblair Mar 1, 2017
722a51c
update example
rwblair Mar 2, 2017
f4ab57e
remake specs
rwblair Mar 2, 2017
f28151b
add more descriptions
rwblair Mar 2, 2017
40edcbf
fix output_average_image not taking user defined file name
rwblair Mar 2, 2017
5c4193b
add examples of using AntsMotionCorr to take average of an image
rwblair Mar 2, 2017
a2ca34e
add note about lack of origin of rotation for motioncorrection conver…
rwblair Mar 2, 2017
6935720
remove test wat
rwblair Mar 2, 2017
24d1e4e
Raise error if unable to format trasnformation model argument
rwblair Mar 2, 2017
42f85df
add write frame displacements arguments to antsmotioncorr. Also updat…
rwblair Mar 3, 2017
2334489
update list arguments to format as a string to properly account for s…
rwblair Mar 3, 2017
644ce4c
udpate antsmotioncorr example
rwblair Mar 3, 2017
c73fb2d
Merge branch 'master' of github.com:nipy/nipype into add_antsMotionCorr
rwblair Mar 6, 2017
43f0913
remove ants prefix from class names
rwblair Mar 10, 2017
2c3833d
update spec test for new class name
rwblair Mar 10, 2017
ebebf70
update specs for new class names
rwblair Mar 10, 2017
8b9c20a
add test for Matrix2FSLParams
rwblair Mar 10, 2017
ebd5350
remove old auto tests
rwblair Mar 10, 2017
8287744
add preprocess functions to init
rwblair Mar 13, 2017
deba31a
remove unnecessary _extant function
rwblair Mar 13, 2017
045e798
remove old auto test
rwblair Mar 13, 2017
4ffee61
Merge branch 'master' of github.com:nipy/nipype into add_antsMotionCorr
rwblair Mar 13, 2017
c5e90a1
switch matrix conversion to use nibabel
rwblair Mar 15, 2017
2930b24
Merge branch 'master' of github.com:nipy/nipype into add_antsMotionCorr
rwblair Mar 15, 2017
95313e1
update matrix conversion names, fix typo, make output file naming sim…
rwblair Mar 15, 2017
5c1e3f6
update init to match new names in preprocess
rwblair Mar 15, 2017
01bc07d
fix spelling mistake
rwblair Mar 15, 2017
32968cd
still need _list_outputs
rwblair Mar 15, 2017
ab74434
correct input and output names in list_outputs
rwblair Mar 15, 2017
7401ad0
update motioncorr2fslparams test to check to see if the original and …
rwblair Mar 16, 2017
56ebd4a
switch file operatations to use numpy in test_MotionCorr2FSLParams
rwblair Mar 16, 2017
01c60e8
Merge branch 'master' of github.com:nipy/nipype into add_antsMotionCorr
rwblair Mar 16, 2017
a13a7dd
switch file operations in MotionCorr2FslParams to use numpy savetxt
rwblair Mar 16, 2017
696aa4a
have newly generated parameters be saved as arrays not strings so tha…
rwblair Mar 16, 2017
77250b2
add in c3d transformation - broken
rwblair Mar 17, 2017
bd73913
Merge remote-tracking branch 'upstream/master' into add_antsMotionCorr
oesteban Mar 21, 2017
ad0aecb
Merge remote-tracking branch 'upstream/master' into add_antsMotionCorr
oesteban Mar 22, 2017
4099cef
Merge branch 'add_antsMotionCorr' of https://github.com/rwblair/nipyp…
oesteban Mar 22, 2017
d0d03b0
use numpy to handle matrices
oesteban Mar 22, 2017
d8786aa
add moco2itk
oesteban Mar 23, 2017
156a5bb
Merge branch 'master' into add_antsMotionCorr
oesteban Apr 30, 2017
e87346b
add doctest, use name_source when possible
oesteban Apr 30, 2017
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2 changes: 2 additions & 0 deletions nipype/interfaces/ants/__init__.py
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Expand Up @@ -3,6 +3,8 @@
# vi: set ft=python sts=4 ts=4 sw=4 et:

"""Top-level namespace for ants."""
# Preprocessing Programs
from .preprocess import MotionCorr2FSLParams, MotionCorr, MotionCorrStats

# Registraiton programs
from .registration import ANTS, Registration
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