-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathrun_all.py
147 lines (131 loc) · 4.35 KB
/
run_all.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
import re
import subprocess
from pathlib import Path
import sys
import pandas as pd
def get_age(index, subject_info):
age = subject_info.at[index, "scan_age"]
if age > 36:
age = 36
return f"{age:.0f}" # round to whole week
path_derivatives = Path("/data/p_02915/dhcp_derivatives_SPOT/Neonates")
path_anat_data = Path("/data/pt_02880/Package_1225541/fmriresults01/rel3_derivatives/rel3_dhcp_anat_pipeline") # path_derivatives / "dhcp_anat_pipeline"
path_func_data = Path("/data/pt_02880/Package_1225541/fmriresults01/rel3_derivatives/rel3_dhcp_fmri_pipeline/") # path_derivatives / "dhcp_fmri_pipeline"
path_output_data = path_derivatives / "dhcp_surface"
path_templates = Path("/data/p_02915/templates")
# templates
name_volume_template_40wks = "dhcp40wk"
file_volume_template_40wks = (
path_templates
/ "template_augmentedvolumetricatlas_dhcp/atlas/T2/template-40.nii.gz"
)
name_surface_template = "dhcpSym"
path_surface_template = (
path_templates
/ "template_corticalsurfaceneonatessym_williams2023_dhcp/dhcpSym_template/"
)
path_fsaverage = path_templates / "template_fsaverage/fsaverage"
path_HCPtemplates_standardmeshatlases = (
"/data/u_yoos_software/HCPpipelines/"
"global/templates/standard_mesh_atlases"
)
# --------------PATHS TO SOFTWARE--------------------------------------------------
path_newmsm = "/data/p_02915/Chello/fsl/bin/msm-env/bin/newmsm"
path_wbcommand = "/bin/wb_command"
path_mirtk = "/afs/cbs.mpg.de/software/mirtk/0.20231123/debian-bullseye-amd64/bin/mirtk"
subject_info = pd.read_csv('/data/p_02915/SPOT/dhcp_subj_path_SPOT_less_37_v2.csv')
sub_num = int(sys.argv[1])
script_dir = Path(__file__).resolve().parent
surfaceprep_script = str(script_dir / "01_dataprep" / "run_surfaceprep.sh")
ccfmodel_script = str(script_dir / "02_ccfanalysis" / "run_model.py")
fillretinotopy_script = str(
script_dir / "03_retinotopyanalysis" / "analyse_retinotopy.py"
)
fillretinotopy_script_2 = str(
script_dir / "03_retinotopyanalysis" / "filter_sigma.py"
)
project_results_script = str(
script_dir / "03_retinotopyanalysis" / "project_ccf_to_fsaverage.sh"
)
project_results_script_2 = str(
script_dir / "03_retinotopyanalysis" / "project_correlation_to_fsaverage.sh"
)
for index, row in subject_info.iloc[sub_num:sub_num + 1].iterrows():
sub_id = subject_info.at[index, "sub_id"]
sess_id = subject_info.at[index, "sess_id"]
sub = sub_id.replace('sub-','')
ses = sess_id.replace('ses-','')
# for sub, ses in sub_ses_todo:
path_scaninfo = path_anat_data / f"sub-{sub}" / f"sub-{sub}_sessions.tsv"
age = get_age(index, subject_info)
#cmd_surfaceprep = [
# str(option)
# for option in [
# surfaceprep_script,
# sub,
# ses,
# age,
# path_derivatives,
# path_anat_data,
# path_func_data,
# path_output_data,
# file_volume_template_40wks,
# name_volume_template_40wks,
# path_surface_template,
# name_surface_template,
# path_HCPtemplates_standardmeshatlases,
# path_fsaverage,
# path_newmsm,
# path_wbcommand,
# path_mirtk,
# ]
#]
#subprocess.run(cmd_surfaceprep, check=True)
cmd_ccfmodel = [
"python",
ccfmodel_script,
"-d",
str(path_derivatives),
"-sub",
sub,
"-ses",
ses,
"-th",
'0'
]
subprocess.run(cmd_ccfmodel, check=True)
cmd_fillretinotopy = [
"python",
fillretinotopy_script,
"-d",
str(path_derivatives),
"-sub",
sub,
"-ses",
ses,
"-th",
'00',
]
subprocess.run(cmd_fillretinotopy, check=True)
cmd_project_results = [
project_results_script,
sub,
ses,
str(path_anat_data),
str(path_derivatives),
str(path_HCPtemplates_standardmeshatlases),
str(path_fsaverage),
str(path_wbcommand),
]
subprocess.run(cmd_project_results, check=True)
cmd_project_results2 = [
project_results_script_2,
sub,
ses,
str(path_anat_data),
str(path_derivatives),
str(path_HCPtemplates_standardmeshatlases),
str(path_fsaverage),
str(path_wbcommand),
]
subprocess.run(cmd_project_results2, check=True)