C-PAC-v1.0.0.zip
FCP-INDI-C-PAC-cdeb072
.gitignore
313 Bytes
CPAC
AWS
aws_utils.py
14.7 kB
GUI
__init__.py
40 Bytes
interface
__init__.py
0 Bytes
pages
__init__.py
1.5 kB
alff.py
2.2 kB
anatomical.py
7.7 kB
centrality.py
6.5 kB
dualreg.py
1.7 kB
filtering.py
1.0 kB
functional_tab.py
10.3 kB
group_analysis.py
10.6 kB
motion.py
1.8 kB
nuisance.py
8.2 kB
reho.py
2.3 kB
sca.py
4.4 kB
settings.py
14.4 kB
smoothing.py
2.2 kB
timeseries.py
13.0 kB
vmhc.py
3.8 kB
utils
__init__.py
451 Bytes
constants.py
2.7 kB
custom_control.py
44.2 kB
generic_class.py
17.8 kB
modelDesign_window.py
27.8 kB
modelconfig_window.py
50.1 kB
validator.py
1.8 kB
windows
__init__.py
56 Bytes
config_window.py
43.5 kB
dataconfig_window.py
19.1 kB
main_window.py
33.5 kB
mainUI.py
435 Bytes
resources
config_parameters.txt
6.5 kB
html
_images
abide_adhd_structure.png
43.9 kB
after_warp_gui.png
91.7 kB
alff_gui.png
93.2 kB
alff_zuo_difference.png
359.5 kB
alff_zuo_trt.png
461.6 kB
anat_prepro_schematic.png
76.4 kB
anat_reg_gui.png
136.9 kB
basc_manu_schematic.png
369.6 kB
centrality_gui.png
178.7 kB
centrality_zuo_cover.png
239.3 kB
centrality_zuo_map.png
726.4 kB
cloud_gui_sge.png
142.7 kB
cloud_x2go.png
70.8 kB
compute_gui.png
122.2 kB
cwas.png
111.5 kB
cwas_shehzad_brains.png
363.4 kB
cwas_shehzad_schematic.png
260.4 kB
cyberduck.png
94.4 kB
derivs_outputs.png
49.8 kB
fcon_structure.png
27.9 kB
func_to_anat_reg.png
140.4 kB
func_to_mni_reg.png
144.8 kB
functional_preprocessing.png
74.2 kB
ga_contrast_csv.png
9.5 kB
ga_contrast_ftest.png
10.0 kB
ga_contrasts.png
41.9 kB
ga_contrasts_populated.png
54.4 kB
ga_main.png
88.9 kB
ga_model_setup.png
95.1 kB
ga_model_setup_populated.png
143.9 kB
main_gui.png
67.1 kB
main_gui_checks.png
79.0 kB
median_angle.png
92.1 kB
nki-rs_template.png
146.2 kB
nuisance.png
109.2 kB
output_gui.png
144.8 kB
processing_workflow.png
106.6 kB
registration.png
179.5 kB
reho_gui.png
114.2 kB
reho_voxel_schematic.png
91.0 kB
reho_yan_dmn.png
144.1 kB
roi_timeseries.png
79.3 kB
sca_gui.png
128.8 kB
sca_map.png
110.1 kB
scrubbing_gui.png
96.2 kB
seg_gui.png
110.4 kB
segmentation.png
74.6 kB
smoothing.png
71.6 kB
subject_list_gui.png
77.9 kB
symlink_structure.png
27.7 kB
tf_gui.png
93.6 kB
ts_options.png
106.3 kB
tse_gui.png
107.8 kB
vmhc_gee_schematic.png
120.3 kB
vmhc_gui.png
131.7 kB
vmhc_stark_regions.png
241.0 kB
vmhc_zuo_smoothing.png
408.2 kB
voxel_timeseries.png
95.7 kB
_sources
.doctrees
_static
1400.doctree
3.1 kB
2500.doctree
2.8 kB
645.doctree
2.8 kB
dti.doctree
3.6 kB
alff.doctree
29.0 kB
anat.doctree
36.9 kB
basc.doctree
28.3 kB
benchmark.doctree
24.3 kB
centrality.doctree
42.4 kB
compute_config.doctree
10.5 kB
cwas.doctree
22.6 kB
data_config.doctree
32.0 kB
derivs.doctree
14.1 kB
dual_reg.doctree
18.1 kB
files.doctree
27.9 kB
fsl_ga.doctree
31.6 kB
func.doctree
19.2 kB
help.doctree
5.6 kB
index.doctree
24.5 kB
install.doctree
108.7 kB
motion.doctree
37.0 kB
nuisance.doctree
39.0 kB
outputs.doctree
21.4 kB
preproc.doctree
6.7 kB
reho.doctree
27.6 kB
rnotes.doctree
95.3 kB
sca.doctree
12.8 kB
slice.doctree
32.2 kB
smoothing.doctree
16.0 kB
temporal.doctree
25.3 kB
tse.doctree
16.7 kB
use.doctree
31.6 kB
vmhc.doctree
26.8 kB
_images
abide_adhd_structure.png
43.9 kB
after_warp_gui.png
91.7 kB
alff_gui.png
93.2 kB
alff_zuo_difference.png
359.5 kB
alff_zuo_trt.png
461.6 kB
anat_prepro_schematic.png
76.4 kB
anat_reg_gui.png
136.9 kB
basc_manu_schematic.png
369.6 kB
centrality_gui.png
178.7 kB
centrality_zuo_cover.png
239.3 kB
centrality_zuo_map.png
726.4 kB
cloud_gui_sge.png
142.7 kB
cloud_x2go.png
70.8 kB
compute_gui.png
122.2 kB
cwas.png
111.5 kB
cwas_shehzad_brains.png
363.4 kB
cwas_shehzad_schematic.png
260.4 kB
cyberduck.png
117.2 kB
derivs_outputs.png
49.8 kB
fcon_structure.png
27.9 kB
func_to_anat_reg.png
140.4 kB
func_to_mni_reg.png
144.8 kB
functional_preprocessing.png
74.2 kB
ga_contrast_csv.png
9.5 kB
ga_contrast_ftest.png
10.0 kB
ga_contrasts.png
42.1 kB
ga_contrasts_populated.png
54.7 kB
ga_main.png
88.9 kB
ga_model_setup.png
95.1 kB
ga_model_setup_populated.png
141.4 kB
main_gui.png
67.1 kB
main_gui_checks.png
79.0 kB
median_angle.png
92.1 kB
nki-rs_template.png
146.2 kB
nuisance.png
109.2 kB
output_gui.png
144.8 kB
processing_workflow.png
106.6 kB
registration.png
179.5 kB
reho_gui.png
114.2 kB
reho_voxel_schematic.png
91.0 kB
reho_yan_dmn.png
144.1 kB
roi_timeseries.png
79.3 kB
sca_gui.png
128.8 kB
sca_map.png
110.1 kB
scrubbing_gui.png
96.2 kB
seg_gui.png
110.4 kB
segmentation.png
74.6 kB
slice_time.png
97.1 kB
smoothing.png
71.6 kB
subject_list_gui.png
77.9 kB
symlink_structure.png
27.7 kB
tf_gui.png
93.6 kB
ts_options.png
106.3 kB
tse_gui.png
107.8 kB
vmhc_gee_schematic.png
120.3 kB
vmhc_gui.png
131.7 kB
vmhc_stark_regions.png
241.0 kB
vmhc_zuo_smoothing.png
408.2 kB
voxel_timeseries.png
95.7 kB
_static
1400.html
3.2 kB
1400.txt
388 Bytes
2500.html
3.1 kB
2500.txt
247 Bytes
645.html
3.1 kB
645.txt
228 Bytes
ajax-loader.gif
673 Bytes
basic.css
8.5 kB
cmi_logo.jpg
25.0 kB
comment-bright.png
947 Bytes
comment-close.png
1.1 kB
comment.png
840 Bytes
cpac_logo.jpg
15.3 kB
data_config_abide.yaml
379 Bytes
data_config_abide_s3.yaml
490 Bytes
data_config_adhd.yaml
378 Bytes
data_config_adhd_s3.yaml
471 Bytes
data_config_fcon.yaml
380 Bytes
data_config_nki.yaml
379 Bytes
data_config_nki_s3.yaml
383 Bytes
doctools.js
6.7 kB
down-pressed.png
291 Bytes
down.png
257 Bytes
dti.txt
608 Bytes
example_phenotypic_file.csv
212 Bytes
file.png
312 Bytes
indi_logo.jpg
8.5 kB
jquery.js
252.9 kB
minus.png
90 Bytes
multiscan_parameters_nki.csv
493 Bytes
nature.css
4.2 kB
nki_cmi.png
26.6 kB
nki_logo.jpg
14.5 kB
nyu_logo.jpg
14.8 kB
outputs
anatomical
registration.csv
3.0 kB
segmentation.csv
833 Bytes
derivatives.csv
4.2 kB
outputs.csv
2.2 kB
params
afterwarp_config.csv
343 Bytes
alff_config.csv
516 Bytes
anat_config.csv
1.4 kB
centrality_config.csv
3.2 kB
compute_config.csv
908 Bytes
data_config.csv
2.2 kB
fta_config.csv
1.1 kB
ftm_config.csv
1.1 kB
group_config.csv
4.7 kB
medianangle_config.csv
293 Bytes
nuisance_config.csv
907 Bytes
output_config.csv
1.3 kB
reho_config.csv
354 Bytes
sca_config.csv
527 Bytes
scrubbing_config.csv
552 Bytes
seg_config.csv
1.2 kB
spatialregression_config.csv
538 Bytes
tf_config.csv
378 Bytes
ts_config.csv
704 Bytes
tse_roiavg_config.csv
939 Bytes
tse_seeds_config.csv
962 Bytes
tse_voxelwiseavg_config.csv
978 Bytes
vmhc_config.csv
1.2 kB
plus.png
90 Bytes
pygments.css
3.9 kB
scan_parameters_abide.csv
674 Bytes
scan_parameters_adhd.csv
357 Bytes
scan_parameters_fcon.csv
1.2 kB
searchtools.js
17.9 kB
subject_list_group_analysis.txt
64 Bytes
underscore.js
41.4 kB
up-pressed.png
289 Bytes
up.png
250 Bytes
websupport.js
25.2 kB
after_warp.txt
4.6 kB
alff.txt
6.2 kB
anat.txt
7.5 kB
benchmark.txt
6.0 kB
centrality.txt
11.1 kB
cloud.txt
23.6 kB
compute_config.txt
6.7 kB
conf.py
8.1 kB
derivatives.txt
510 Bytes
docker.txt
831 Bytes
files.txt
2.4 kB
func.txt
10.5 kB
futuredocs
basc.txt
6.2 kB
cwas.txt
6.9 kB
tse.txt
1.4 kB
group_analysis.txt
12.1 kB
help.txt
4.7 kB
index.txt
5.0 kB
install.txt
17.6 kB
nuisance.txt
24.0 kB
output_config.txt
2.4 kB
pipeline_config.txt
4.5 kB
reho.txt
5.7 kB
remove_links.sh
1.1 kB
rnotes.txt
18.9 kB
running.txt
4.7 kB
sca.txt
6.3 kB
subject_list_config.txt
12.1 kB
tse.txt
3.0 kB
vmhc.txt
6.2 kB
_static
1400.html
3.2 kB
1400.txt
388 Bytes
2500.html
3.1 kB
2500.txt
247 Bytes
645.html
3.1 kB
645.txt
228 Bytes
ajax-loader.gif
673 Bytes
alert_info_32.png
1.2 kB
alert_warning_32.png
1.4 kB
basic.css
8.5 kB
bg-page.png
84 Bytes
bullet_orange.png
185 Bytes
cmi_logo.jpg
25.0 kB
comment-bright.png
947 Bytes
comment-close.png
1.1 kB
comment.png
840 Bytes
cpac_logo.jpg
15.3 kB
data_config_abide.yaml
379 Bytes
data_config_abide_s3.yaml
490 Bytes
data_config_adhd.yaml
378 Bytes
data_config_adhd_s3.yaml
471 Bytes
data_config_fcon.yaml
380 Bytes
data_config_nki.yaml
379 Bytes
data_config_nki_s3.yaml
383 Bytes
doctools.js
6.7 kB
down-pressed.png
291 Bytes
down.png
273 Bytes
dti.html
2.7 kB
dti.txt
608 Bytes
example_phenotypic_file.csv
212 Bytes
file.png
312 Bytes
haiku.css
6.7 kB
indi_logo.jpg
8.5 kB
jquery.js
252.9 kB
minus.png
106 Bytes
multiscan_parameters_nki.csv
493 Bytes
nature.css
4.2 kB
nki_cmi.png
26.6 kB
nki_logo.jpg
14.5 kB
nyu_logo.jpg
14.8 kB
outputs
anatomical
registration.csv
3.0 kB
segmentation.csv
833 Bytes
derivatives.csv
4.2 kB
outputs.csv
2.2 kB
params
afterwarp_config.csv
343 Bytes
alff_config.csv
516 Bytes
anat_config.csv
1.4 kB
centrality_config.csv
3.2 kB
compute_config.csv
908 Bytes
data_config.csv
2.2 kB
fta_config.csv
1.1 kB
ftm_config.csv
1.1 kB
group_config.csv
4.7 kB
medianangle_config.csv
293 Bytes
nuisance_config.csv
907 Bytes
output_config.csv
1.3 kB
reho_config.csv
354 Bytes
sca_config.csv
527 Bytes
scrubbing_config.csv
552 Bytes
seg_config.csv
1.2 kB
spatialregression_config.csv
538 Bytes
tf_config.csv
378 Bytes
ts_config.csv
704 Bytes
tse_roiavg_config.csv
939 Bytes
tse_seeds_config.csv
962 Bytes
tse_voxelwiseavg_config.csv
978 Bytes
vmhc_config.csv
1.2 kB
plus.png
106 Bytes
pygments.css
3.9 kB
scan_parameters_abide.csv
674 Bytes
scan_parameters_adhd.csv
357 Bytes
scan_parameters_fcon.csv
1.2 kB
searchtools.js
17.9 kB
subject_list_group_analysis.html
2.1 kB
subject_list_group_analysis.txt
64 Bytes
underscore.js
41.4 kB
up-pressed.png
289 Bytes
up.png
266 Bytes
websupport.js
25.2 kB
after_warp.html
9.0 kB
alff.html
11.4 kB
anat.html
15.1 kB
benchmark.html
11.7 kB
centrality.html
19.6 kB
cloud.html
34.5 kB
compute_config.html
12.2 kB
derivatives.html
3.9 kB
docker.html
3.8 kB
files.html
7.7 kB
func.html
20.9 kB
genindex.html
2.1 kB
group_analysis.html
23.8 kB
help.html
8.5 kB
index.html
17.4 kB
install.html
28.1 kB
nuisance.html
34.8 kB
objects.inv
201 Bytes
output_config.html
7.2 kB
pipeline_config.html
9.9 kB
reho.html
10.6 kB
rnotes.html
27.6 kB
running.html
10.1 kB
sca.html
12.0 kB
search.html
3.0 kB
searchindex.js
45.3 kB
subject_list_config.html
22.6 kB
tse.html
10.0 kB
vmhc.html
12.4 kB
images
add1.jpeg
640 Bytes
add1.png
1.7 kB
add2.png
3.0 kB
add3.jpg
18.8 kB
aquachecked.ico
1.4 kB
aquaflagged.ico
1.4 kB
aquanotchecked.ico
1.4 kB
aquanotflagged.ico
1.4 kB
checked.ico
634 Bytes
cpac_logo.jpg
15.3 kB
cpac_logo2.jpg
4.9 kB
cpac_logo_2.jpg
5.8 kB
cpac_new_logo.png
22.9 kB
cpac_rgb.png
16.0 kB
flagged.ico
634 Bytes
foder10.gif
3.7 kB
folder.bmp
4.0 kB
folder.png
8.9 kB
folder10.png
1.7 kB
folder2.bmp
246 Bytes
folder3.gif
615 Bytes
folder4.gif
1.0 kB
folder5.gif
365 Bytes
folder6.jpeg
551 Bytes
folder7.gif
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folder8.jpeg
657 Bytes
folder9.gif
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help.png
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minus1.ico
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minus2.ico
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minus3.ico
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minus4.ico
258 Bytes
minus5.ico
1.3 kB
minus9.jpg
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notchecked.ico
634 Bytes
notflagged.ico
634 Bytes
plus1.ico
1.3 kB
plus10.jpg
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plus11.jpg
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plus12.jpg
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plus13.jpeg
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plus2.ico
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plus3.ico
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plus4.ico
258 Bytes
plus5.ico
1.3 kB
plus6.jpeg
384 Bytes
plus7.png
544 Bytes
plus8.jpeg
3.6 kB
plus9.jpeg
2.9 kB
pipeline_names.py
2.0 MB
README.txt
0 Bytes
__init__.py
2.0 kB
_build.py
2.4 kB
alff
__init__.py
389 Bytes
alff.py
7.7 kB
utils.py
3.3 kB
anat_preproc
__init__.py
45 Bytes
anat_preproc.py
5.4 kB
tests
__init__.py
122 Bytes
test_anat_preproc.py
8.1 kB
basc
__init__.py
805 Bytes
basc.py
16.9 kB
python_ncut_lib.py
9.1 kB
tests
__init__.py
0 Bytes
test_basc.py
4.8 kB
utils.py
8.6 kB
cwas
__init__.py
265 Bytes
cwas.py
11.8 kB
hats.py
2.6 kB
mdmr.py
5.1 kB
subdist.py
1.4 kB
tests
__init__.py
0 Bytes
features
conn-dists_connectir.feature
1.2 kB
conn_multiple.feature
925 Bytes
conn_single.feature
1.0 kB
dists.feature
688 Bytes
mdmrs_connectir.feature
3.3 kB
steps
base_cwas.py
1.1 kB
step_conn-dists_connectir.py
3.1 kB
step_conn_multiple.feature
1.7 kB
step_conn_single.feature
1.2 kB
step_dists.py
997 Bytes
step_mdmrs_connectir.py
2.9 kB
test_cwas.py
10.2 kB
utils.py
3.1 kB
easy_thresh
__init__.py
357 Bytes
easy_thresh.py
18.9 kB
func_preproc
__init__.py
141 Bytes
func_preproc.py
22.6 kB
generate_motion_statistics
__init__.py
889 Bytes
generate_motion_statistics.py
34.5 kB
group_analysis
__init__.py
158 Bytes
group_analysis.py
16.0 kB
info.py
5.0 kB
median_angle
__init__.py
445 Bytes
median_angle.py
9.9 kB
tests
__init__.py
0 Bytes
test_median_angle.py
1.2 kB
network_centrality
__init__.py
1.3 kB
afni_centrality_interfaces.py
7.5 kB
afni_network_centrality.py
6.4 kB
core.py
6.4 kB
resting_state_centrality.py
29.4 kB
tests
calc_centrality.py
4.8 kB
regression_tests.py
3.2 kB
test_a_threshold.py
2.5 kB
test_b_centrality.py
5.4 kB
thresh_and_sum.pyx
3.9 kB
utils.py
20.5 kB
z_score.py
4.2 kB
nuisance
__init__.py
431 Bytes
nuisance.py
21.9 kB
tests
__init__.py
0 Bytes
test_nuisance.py
6.6 kB
utils.py
1.9 kB
pipeline
__init__.py
226 Bytes
cpac_basc_pipeline.py
2.0 kB
cpac_cwas_pipeline.py
1.7 kB
cpac_ga_model_generator.py
36.5 kB
cpac_group_analysis_pipeline.py
26.1 kB
cpac_group_runner.py
32.3 kB
cpac_pipeline.py
235.1 kB
cpac_runner.py
18.4 kB
new_cpac_ga_model_generator.py
30.2 kB
new_cpac_group_runner.py
27.6 kB
qc
__init__.py
39 Bytes
blue.py
2.0 kB
cyan_to_yellow.py
2.0 kB
green.py
2.0 kB
qc.py
7.0 kB
red.py
2.0 kB
red_to_blue.py
2.0 kB
utils.py
65.8 kB
quality_control
README.txt
177 Bytes
registration
__init__.py
796 Bytes
registration.py
42.1 kB
tests
test_registration.py
4.3 kB
utils.py
2.8 kB
reho
__init__.py
236 Bytes
reho.py
3.3 kB
utils.py
7.3 kB
resources
bootstrap
css
.Rhistory
0 Bytes
bootstrap-responsive.css
22.1 kB
bootstrap-responsive.min.css
16.8 kB
bootstrap.css
127.4 kB
bootstrap.min.css
106.0 kB
img
glyphicons-halflings-white.png
8.8 kB
glyphicons-halflings.png
12.8 kB
js
bootstrap.js
62.0 kB
bootstrap.min.js
28.6 kB
jquery.js
274.1 kB
jquery.min.js
93.1 kB
kul-substitute.js
1.7 kB
kul-substitute.min.js
652 Bytes
templates
MNI152_Edge_AllTissues.nii.gz
961.2 kB
cpac_runner.html
12.1 kB
logger_group_index.html
7.6 kB
logger_subject_index.html
3.4 kB
sca
README.txt
0 Bytes
__init__.py
318 Bytes
sca.py
13.8 kB
tests
__init__.py
122 Bytes
test_sca.py
16.3 kB
utils.py
5.7 kB
scrubbing
__init__.py
225 Bytes
scrubbing.py
7.9 kB
seg_preproc
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seg_preproc.py
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setup.py
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timeseries
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timeseries_analysis.py
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utils
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__init__.py
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bids_metadata.py
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build_sublist.py
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configuration.py
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create_all_qc.py
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create_flame_model_files.py
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create_fsl_model.py
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create_group_analysis_info_files.py
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datasource.py
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extract_data.py
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extract_data_multiscan.py
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extract_parameters.py
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pipeline_names.py
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test_init.py
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utils.py
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vmhc
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utils.py
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vmhc.py
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LICENSE
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README.md
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benchmarks
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sca_profiler.py
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build_helpers.py
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configs
config_fsl.yml
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data_config.yml
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pipeline_config.yml
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scan_parameters.csv
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scan_parameters_multiscan.csv
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doc
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installation.rst
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testing.rst
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workflow_documentation.rst
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alff.dot.png
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alff_detailed.dot.png
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basc.dot.png
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create_temporal_regression.png
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cwas.dot.png
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cwas_detailed.dot.png
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detailed_graph_create_temporal_regression.png
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easy_thresh_detailed.dot.png
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fristons_twenty_four.dot.png
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sca_detailed_graph.dot.png
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surface_registration.dot.png
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target_angle.dot.png
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target_angle_detailed.dot.png
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zscore.dot.png
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zscore_detailed.dot.png
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index.rst
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make.bat
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pipeline
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sphinxext
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MANIFEST.in
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PKG-INFO
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README.txt
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__init__.py
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comment_eater.py
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compiler_unparse.py
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docscrape.py
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docscrape_sphinx.py
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numpydoc.py
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phantom_import.py
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plot_directive.py
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setup.cfg
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setup.py
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tests
test_docscrape.py
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traitsdoc.py
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workflows
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alff.rst
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anat_preproc.rst
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basc.rst
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cwas.rst
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easy_thresh.rst
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func_preproc.rst
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generate_motion_statistics.rst
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group_analysis.rst
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index.rst
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median_angle.rst
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network_centrality.rst
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nuisance.rst
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registration.rst
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sca.rst
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scrubbing.rst
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seg_preproc.rst
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timeseries.rst
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vmhc.rst
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scripts
cpac_centrality.py
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cpac_extract_parameters.py
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cpac_gui
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cpac_install.sh
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cpac_run.py
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cpac_setup.py
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setup.py
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test
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README.txt
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__init__.py
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reg
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network_centrality
eigenvector_golden.py
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resting_state_centrality_test.py
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utils.py
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templates
data_config_template.yml
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test_all.py
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test_trivial.py
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unit
GUI
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interface
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windows
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config_window_test.py
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dataconfig_window_test.py
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__init__.py
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nipype
datasink_test.py
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pipeline
__init__.py
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cpac_pipeline_test.py
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utils
build_sublist_test.py
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