def vta_composite():
preprocessing.bruker("/home/chymera/ni_data/ofM.vta/",
workflow_name="composite",
very_nasty_bruker_delay_hack=False,
negative_contrast_agent=True,
functional_blur_xy=4,
functional_registration_method="composite")
def cbv_composite(
data_path,
workflow_name,
preprocessing_dir="preprocessing",
l1_dir="l1",
):
preprocessing.bruker(
data_path,
#exclude_measurements=['20151027_121613_4013_1_1'],
functional_scan_types=["EPI_CBV_chr_longSOA", "EPI_CBV_jb_long"],
#subjects=["4007","4008","4011","4012","5687","5688","5695","5689","5690","5691","5703","5704","5706"],
#subjects=["4007","4008","5687","5688","5704",
# "5692","6262","5694","5700","6255","5699"],
#subjects=["4001","4011","5703","5706",],
workflow_name=workflow_name,
lowpass_sigma=2,
highpass_sigma=225,
very_nasty_bruker_delay_hack=True,
negative_contrast_agent=True,
functional_blur_xy=.4,
functional_registration_method="composite",
keep_work=True,
template="~/ni_data/templates/DSURQEc_200micron_average.nii",
registration_mask="~/ni_data/templates/DSURQEc_200micron_mask.nii.gz",
actual_size=True,
verbose=True,
)
glm.l1(
path.join(data_path, preprocessing_dir, workflow_name),
workflow_name=workflow_name,
# include={"subjects":["5689","5690","5691"]},
habituation="confound",
mask="/home/chymera/ni_data/templates/DSURQEc_200micron_mask.nii.gz",
keep_work=True,
)
glm.l2_common_effect(
path.join(data_path, l1_dir, workflow_name),
workflow_name="composite_subjects",
exclude={
"scans": ["EPI_BOLD_"],
},
groupby="subject",
keep_work=True,
mask="/home/chymera/ni_data/templates/DSURQEc_200micron_mask.nii.gz",
)
glm.l2_common_effect(
path.join(data_path, l1_dir, workflow_name),
workflow_name="composite_sessions_responders",
exclude={
"scans": ["EPI_BOLD_"],
"subjects": [
"4001", "4002", "4003", "4004", "4006", "4008", "4009", "5674",
"5703", "5704", "5706"
]
},
groupby="session",
keep_work=True,
mask="/home/chymera/ni_data/templates/DSURQEc_200micron_mask.nii.gz",
)
def dr_composite():
preprocessing.bruker("/home/chymera/ni_data/ofM.dr/",
exclude_measurements=['20151027_121613_4013_1_1'],
workflow_name="composite",
very_nasty_bruker_delay_hack=True,
negative_contrast_agent=True,
functional_blur_xy=4,
functional_registration_method="composite")
glm.l1("~/ni_data/ofM.dr/preprocessing/composite",
workflow_name="composite",
include={"subjects": [i for i in range(4001, 4010)] + [4011, 4012]},
habituation="confound",
mask="/home/chymera/ni_data/templates/ds_QBI_chr_bin.nii.gz",
keep_work=True)
glm.l1(
"~/ni_data/ofM.dr/preprocessing/composite",
workflow_name="composite_dr",
include={"subjects": [i for i in range(4001, 4010)] + [4011, 4012]},
habituation="confound",
mask="/home/chymera/ni_data/templates/roi/f_dr_chr_bin.nii.gz",
)
glm.l2_common_effect("~/ni_data/ofM.dr/l1/composite",
workflow_name="subjectwise_composite",
groupby="subject")
glm.l2_common_effect("~/ni_data/ofM.dr/l1/composite",
workflow_name="sessionwise_composite",
groupby="session",
exclude={
"subjects": [
"4001", "4002", "4003", "4004", "4005",
"4006", "4009", "4011", "4013"
]
})
glm.l2_common_effect(
"~/ni_data/ofM.dr/l1/composite",
workflow_name="sessionwise_composite_w4011",
groupby="session",
exclude={
"subjects":
["4001", "4002", "4003", "4004", "4005", "4006", "4009", "4013"]
})
def rs(
data_path="~/ni_data/_test/",
workflow_name="functional_registration",
preprocessing_dir="preprocessing",
):
preprocessing.bruker(
data_path,
functional_scan_types=[
"EPI_CBV",
],
structural_scan_types=-1,
workflow_name=workflow_name,
lowpass_sigma=2,
highpass_sigma=225,
functional_blur_xy=.4,
functional_registration_method="functional",
keep_work=True,
template="~/ni_data/templates/DSURQEc_200micron_average.nii",
registration_mask="~/ni_data/templates/DSURQEc_200micron_mask.nii.gz",
actual_size=True,
)