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Add thr pipeline #20

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merged 6 commits into from
Jun 17, 2024
Merged

Add thr pipeline #20

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851cf70
added skull_mask_thr as an option
davidmeunier79 Jun 6, 2024
5ccbabb
robustt1
davidmeunier79 Jun 11, 2024
36047c3
mesh_t1_skull
davidmeunier79 Jun 11, 2024
4b896ec
segbrain
davidmeunier79 Jun 12, 2024
24b5893
pad_template + robust_reg
davidmeunier79 Jun 17, 2024
731ed1d
flakE8 + pip install Cython
davidmeunier79 Jun 17, 2024
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1 change: 0 additions & 1 deletion .github/workflows/check_on_PR.yml
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Expand Up @@ -27,7 +27,6 @@ jobs:
sudo apt-get install build-essential graphviz libgraphviz-dev
pip install --upgrade pygraphviz graphviz


# pip install --no-deps --index-url https://test.pypi.org/simple/ --pre macapype

pip install -e .
Expand Down
4 changes: 2 additions & 2 deletions setup.py
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Expand Up @@ -4,8 +4,8 @@
import re
from setuptools import find_packages, setup

required_packages = [
"macapype"]
required_packages = ["Cython",
"macapype"]

verstr = "unknown"
try:
Expand Down
39 changes: 39 additions & 0 deletions skullTo3d/pipelines/rename.py
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Expand Up @@ -197,3 +197,42 @@ def rename_all_skull_t1_derivatives(params, main_workflow, segment_pnh_pipe,
main_workflow.connect(
rename_t1_head_mask, 'out_file',
datasink, '@t1_head_mask')

if "t1_skull_fov" in params["skull_t1_pipe"]:

# rename robustt1_skull_stl
rename_robustt1_skull_stl = pe.Node(
niu.Rename(), name="rename_robustt1_skull_stl")

rename_robustt1_skull_stl.inputs.format_string = \
pref_deriv + "_desc-robustt1_skullmask"
rename_robustt1_skull_stl.inputs.parse_string = parse_str
rename_robustt1_skull_stl.inputs.keep_ext = True

main_workflow.connect(
skull_t1_pipe, 'outputnode.robustt1_skull_stl',
rename_robustt1_skull_stl, 'in_file')

main_workflow.connect(
rename_robustt1_skull_stl, 'out_file',
datasink, '@robustt1_skull_stl')

# rename stereo_robustt1_skull_mask
rename_stereo_robustt1_skull_mask = pe.Node(
niu.Rename(), name="rename_stereo_robustt1_skullmask")

rename_stereo_robustt1_skull_mask.inputs.format_string = \
pref_deriv + "_space-stereo_desc-robustt1_skullmask"

rename_stereo_robustt1_skull_mask.inputs.parse_string = \
parse_str

rename_stereo_robustt1_skull_mask.inputs.keep_ext = True

main_workflow.connect(
skull_t1_pipe, 'outputnode.robustt1_skull_mask',
rename_stereo_robustt1_skull_mask, 'in_file')

main_workflow.connect(
rename_stereo_robustt1_skull_mask, 'out_file',
datasink, '@stereo_robustt1_skullmask')
89 changes: 78 additions & 11 deletions skullTo3d/pipelines/skull_pipe.py
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Expand Up @@ -276,30 +276,79 @@ def create_skull_t1_pipe(name="skull_t1_pipe", params={}):
skull_t1_pipe.connect(t1_skull_fill, "out_file",
t1_skull_erode, "in_file")

# mesh_t1_skull_t1 #######
mesh_t1_skull_t1 = pe.Node(
# mesh_t1_skull #######
mesh_t1_skull = pe.Node(
interface=niu.Function(input_names=["nii_file"],
output_names=["stl_file"],
function=wrap_afni_IsoSurface),
name="mesh_t1_skull_t1")
name="mesh_t1_skull")

skull_t1_pipe.connect(t1_skull_erode, "out_file",
mesh_t1_skull_t1, "nii_file")
mesh_t1_skull, "nii_file")

if "t1_skull_fov" in params.keys():

# t1_skull_fov ####### [okey][json]

t1_skull_fov = NodeParams(
interface=RobustFOV(),
params=parse_key(params, "t1_skull_fov"),
name="t1_skull_fov")

skull_t1_pipe.connect(
t1_skull_erode, "out_file",
t1_skull_fov, "in_file")

# t1_skull_clean ####### [okey]
t1_skull_clean = pe.Node(
interface=niu.Function(input_names=["nii_file"],
output_names=["gcc_nii_file"],
function=keep_gcc),
name="t1_skull_clean")

skull_t1_pipe.connect(
t1_skull_fov, "out_roi",
t1_skull_clean, "nii_file")

# mesh_robustt1_skull #######
mesh_robustt1_skull = pe.Node(
interface=niu.Function(input_names=["nii_file"],
output_names=["stl_file"],
function=wrap_afni_IsoSurface),
name="mesh_robustt1_skull")

skull_t1_pipe.connect(
t1_skull_clean, "gcc_nii_file",
mesh_robustt1_skull, "nii_file")

# creating outputnode #######
outputnode = pe.Node(
niu.IdentityInterface(
fields=["t1_skull_mask", "t1_skull_stl", "t1_head_mask"]),
fields=["t1_skull_mask", "t1_skull_stl",
"robustt1_skull_mask", "robustt1_skull_stl",
"t1_head_mask"]),
name='outputnode')

skull_t1_pipe.connect(t1_head_erode, "out_file",
outputnode, "t1_head_mask")
skull_t1_pipe.connect(
t1_head_erode, "out_file",
outputnode, "t1_head_mask")

skull_t1_pipe.connect(mesh_t1_skull_t1, "stl_file",
outputnode, "t1_skull_stl")
skull_t1_pipe.connect(
mesh_t1_skull, "stl_file",
outputnode, "t1_skull_stl")

skull_t1_pipe.connect(t1_skull_erode, "out_file",
outputnode, "t1_skull_mask")
skull_t1_pipe.connect(
t1_skull_erode, "out_file",
outputnode, "t1_skull_mask")

if "t1_skull_fov" in params.keys():
skull_t1_pipe.connect(
t1_skull_fov, "out_roi",
outputnode, "robustt1_skull_mask")

skull_t1_pipe.connect(
mesh_robustt1_skull, "stl_file",
outputnode, "robustt1_skull_stl")

return skull_t1_pipe

Expand Down Expand Up @@ -685,6 +734,21 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}):
skull_petra_pipe.connect(petra_fast, "restored_image",
petra_skull_auto_mask, "img_file")

elif "petra_skull_mask_thr" in params.keys():

# petra_skull_mask_thr
petra_skull_mask_thr = NodeParams(
interface=Threshold(),
params=parse_key(params, 'petra_skull_mask_thr'),
name="petra_skull_mask_thr")

skull_petra_pipe.connect(petra_fast, "restored_image",
petra_skull_mask_thr, "in_file")

skull_petra_pipe.connect(
inputnode, ('indiv_params', parse_key, "petra_skull_mask_thr"),
petra_skull_mask_thr, "indiv_params")

# petra_skull_mask_binary
petra_skull_mask_binary = pe.Node(interface=UnaryMaths(),
name="petra_skull_mask_binary")
Expand All @@ -695,6 +759,9 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}):
if "petra_skull_auto_mask" in params.keys():
skull_petra_pipe.connect(petra_skull_auto_mask, "mask_img_file",
petra_skull_mask_binary, "in_file")
if "petra_skull_mask_thr" in params.keys():
skull_petra_pipe.connect(petra_skull_mask_thr, "out_file",
petra_skull_mask_binary, "in_file")
else:
skull_petra_pipe.connect(petra_fast,
("partial_volume_files", get_elem, 0),
Expand Down
9 changes: 4 additions & 5 deletions workflows/params_segment_macaque_ants_skull.json
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Expand Up @@ -15,14 +15,13 @@
},
"reg_T1_on_template":
{
},
"reg_T1_on_template2":
{
}
},
"resample_T1_pad":
"pad_template":
{
"pad_val": 30
"copy_header" : true,
"operation" : "PadImage",
"op2" : "70"
}
},
"N4debias":
Expand Down
20 changes: 19 additions & 1 deletion workflows/params_segment_marmo_ants_skull.json
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Expand Up @@ -6,21 +6,39 @@
},
"short_preparation_pipe":
{
"aladin_T2_on_T1":{},

"use_T2":{},
"crop_aladin_pipe":
{
"reg_T1_on_template":
{
"nac_flag": true,
"rig_only_flag": true,
"nosym_flag": true,
"ln_val": 12,
"lp_val": 10,
"smoo_r_val": 1.0
},
"reg_T1_on_template2":
{
"rig_only_flag": true,
"nosym_flag": true,
"ln_val": 17,
"lp_val": 15,
"smoo_r_val": 1.0
},
"crop_z_T1":
{
"brainsize": 30
}
},
"resample_T1_pad": {}
"pad_template":
{
"copy_header" : true,
"operation" : "PadImage",
"op2" : "70"
}
},
"fast":
{
Expand Down
5 changes: 4 additions & 1 deletion workflows/segment_petra.py
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Expand Up @@ -172,6 +172,9 @@ def create_main_workflow(data_dir, process_dir, soft, species, subjects,
if 'template' in ssoft:
new_ssoft.remove('template')

if 'robustreg' in ssoft:
new_ssoft.remove('robustreg')

soft = "_".join(new_ssoft)

print("soft: ", soft)
Expand Down Expand Up @@ -285,7 +288,7 @@ def create_main_workflow(data_dir, process_dir, soft, species, subjects,
wf_name += "_CT"

if len(brain_dt) != 0:
wf_name += "_brain"
wf_name += "_segbrain"

if 't1' in brain_dt:
wf_name += "_t1"
Expand Down
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