forked from briancheung/NKI_NYU_Nipype
-
Notifications
You must be signed in to change notification settings - Fork 0
/
resting_preproc.py
executable file
·66 lines (44 loc) · 2.85 KB
/
resting_preproc.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
#!/frodo/shared/epd/bin/python
import e_afni
import sys
import os
import nipype.pipeline.engine as pe
from base import (create_anat_preproc, create_func_preproc,
create_reg_preproc, create_seg_preproc)
def processS():
numCores=int(sys.argv[1])
wfname='resting_preproc'
workflow=pe.Workflow(name=wfname)
anatpreproc=create_anat_preproc()
anatpreproc.inputs.inputspec.anat=os.path.abspath('/home/sharad/Resources/0010052/session_1/anat_1/mprage.nii.gz')
funcpreproc=create_func_preproc()
funcpreproc.inputs.inputspec.rest=os.path.abspath('/home/sharad/Resources/0010052/session_1/rest_1/rest.nii.gz')
funcpreproc.inputs.inputspec.start_idx=0
funcpreproc.inputs.inputspec.stop_idx=175
segpreproc=create_seg_preproc()
segpreproc.inputs.inputspec.PRIOR_CSF = os.path.abspath('/home/sharad/nki_nyu_pipeline/tissuepriors/avg152T1_csf_bin.nii.gz')
segpreproc.inputs.inputspec.PRIOR_WHITE = os.path.abspath('/home/sharad/nki_nyu_pipeline/tissuepriors/avg152T1_white_bin.nii.gz')
segpreproc.inputs.inputspec.standard_res_brain=os.path.abspath('/frodo/shared/RH5_fsl/data/standard/MNI152_T1_3mm_brain.nii.gz')
regpreproc=create_reg_preproc()
regpreproc.inputs.inputspec.standard_res_brain=os.path.abspath('/frodo/shared/RH5_fsl/data/standard/MNI152_T1_3mm_brain.nii.gz')
regpreproc.inputs.inputspec.standard=os.path.abspath('/frodo/shared/RH5_fsl/data/standard/MNI152_T1_3mm.nii.gz')
regpreproc.inputs.inputspec.config_file=os.path.abspath('/frodo/shared/RH5_fsl/etc/flirtsch/T1_2_MNI152_3mm.cnf')
regpreproc.inputs.inputspec.standard_brain_mask_dil=os.path.abspath('/frodo/shared/RH5_fsl/data/standard/MNI152_T1_3mm_brain_mask_dil.nii.gz')
workflow.connect(funcpreproc, 'outputspec.example_func', regpreproc, 'inputspec.example_func')
workflow.connect(anatpreproc, 'outputspec.brain', regpreproc, 'inputspec.brain')
workflow.connect(anatpreproc, 'outputspec.reorient', regpreproc, 'inputspec.reorient')
workflow.connect(funcpreproc, 'outputspec.preprocessed_mask', segpreproc, 'inputspec.preprocessed_mask')
workflow.connect(anatpreproc, 'outputspec.brain', segpreproc, 'inputspec.brain')
workflow.connect(funcpreproc, 'outputspec.example_func', segpreproc, 'inputspec.example_func')
workflow.connect(regpreproc, 'outputspec.highres2example_func_mat', segpreproc, 'inputspec.highres2example_func_mat')
workflow.connect(regpreproc, 'outputspec.stand2highres_warp', segpreproc, 'inputspec.stand2highres_warp')
# workflow.add_nodes([anatpreproc, funcpreproc])
workflow.base_dir='/home/sharad/nki_nyu_pipeline/working_dir'
workflow.run(plugin='MultiProc', plugin_args={'n_procs': numCores})
def main():
if (len(sys.argv) < 2 ):
sys.stderr.write("./resting_preproc.py <Number_of_cores>")
else:
processS()
if __name__ == "__main__":
sys.exit(main())