def create_dcmconvert_pipeline(name='dcmconvert'):
from nipype.pipeline.engine import Node, Workflow
import nipype.interfaces.utility as util
from nipype.interfaces.dcmstack import DcmStack
# workflow
dcmconvert = Workflow(name='dcmconvert')
#inputnode
inputnode = Node(util.IdentityInterface(fields=['dicoms', 'filename']),
name='inputnode')
# outputnode
outputnode = Node(util.IdentityInterface(fields=['nifti']),
name='outputnode')
# conversion node
converter = Node(DcmStack(embed_meta=True), name='converter')
# connections
dcmconvert.connect([(inputnode, converter, [('dicoms', 'dicom_files'),
('filename', 'out_format')]),
(converter, outputnode, [('out_file', 'nifti')])])
return dcmconvert
def test_DcmStack_outputs():
output_map = dict(out_file=dict(), )
outputs = DcmStack.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_DcmStack_outputs():
output_map = dict(out_file=dict(),
)
outputs = DcmStack.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_DcmStack_inputs():
input_map = dict(out_format=dict(),
embed_meta=dict(),
out_ext=dict(usedefault=True,
),
dicom_files=dict(mandatory=True,
),
exclude_regexes=dict(),
include_regexes=dict(),
)
inputs = DcmStack.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def test_DcmStack_inputs():
input_map = dict(
dicom_files=dict(mandatory=True, ),
embed_meta=dict(),
exclude_regexes=dict(),
force_read=dict(usedefault=True, ),
include_regexes=dict(),
out_ext=dict(usedefault=True, ),
out_format=dict(),
)
inputs = DcmStack.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def create_converter_structural_pipeline(working_dir,
ds_dir,
name='converter_struct'):
# initiate workflow
converter_wf = Workflow(name=name)
converter_wf.base_dir = os.path.join(working_dir, 'LeiCA_resting')
# set fsl output
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# inputnode
inputnode = Node(util.IdentityInterface(fields=['t1w_dicom']),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=['t1w']),
name='outputnode')
niftisink = Node(nio.DataSink(), name='niftisink')
niftisink.inputs.base_directory = os.path.join(ds_dir, 'raw_niftis')
# convert to nifti
# todo check if geometry bugs attac. use dcm2nii?
converter_t1w = Node(DcmStack(embed_meta=True), name='converter_t1w')
converter_t1w.plugin_args = {'submit_specs': 'request_memory = 2000'}
converter_t1w.inputs.out_format = 't1w'
converter_wf.connect(inputnode, 't1w_dicom', converter_t1w, 'dicom_files')
# reorient to standard orientation
reor_2_std = Node(fsl.Reorient2Std(), name='reor_2_std')
converter_wf.connect(converter_t1w, 'out_file', reor_2_std, 'in_file')
converter_wf.connect(reor_2_std, 'out_file', outputnode, 't1w')
# save original niftis
converter_wf.connect(reor_2_std, 'out_file', niftisink, 'sMRI')
converter_wf.write_graph(dotfilename='converter_struct',
graph2use='flat',
format='pdf')
return converter_wf
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 9 18:20:32 2015
@author: m131199
"""
import os
os.chdir('/Users/m131199/Downloads/LGG-229/MRI_Hd/axial_T1/')
from nipype.interfaces.dcmstack import DcmStack
stacker = DcmStack()
stacker.inputs.dicom_files = '/Users/m131199/Downloads/LGG-229/MRI_Hd/axial_T1/'
stacker.run()
#result.outputs.out_file
import dcmstack
from glob import glob
src_dcms = glob('/Users/m131199/Downloads/LGG-229/MRI_Hd/axial_T1/*.dcm')
stacks = dcmstack.parse_and_stack(src_dcms)
stack = stacks.values[0]
nii = stack.to_nifti()
nii.to_filename('output.nii.gz')
#import os
#os.chdir('/Users/m131199/Downloads/LGG-229/MRI_Hd/AX_T2_OBL/')
#from nipype.interfaces.freesurfer import DICOMConvert
#cvt = DICOMConvert()
#cvt.inputs.dicom_dir = '/Users/m131199/Downloads/LGG-229/MRI_Hd/AX_T2_OBL/'
#cvt.inputs.file_mapping = [('nifti', '*.nii'), ('info', 'dicom*.txt'), ('dti', '*dti.bv*')]
wf.connect(dcm2nii_dwi, "bvecs", bvecs_rename, "in_file")
bvals_rename = pe.Node(util.Rename(format_string="DTI_mx_137.bvals"),
name="bvals_rename")
wf.connect(dcm2nii_dwi, "bvals", bvals_rename, "in_file")
ds = pe.Node(nio.DataSink(), name="dwi_datasink")
ds.inputs.base_directory = '/scr/kalifornien1/data/nki_enhanced/'
ds.inputs.substitutions = [('_subject_id_', '')]
ds.inputs.regexp_substitutions = [('_others_rename[0-9]*/', '')]
wf.connect(dwi_rename, "out_file", ds, "niftis.@dwi")
wf.connect(bvals_rename, "out_file", ds, "niftis.@bvecs")
wf.connect(bvecs_rename, "out_file", ds, "niftis.@bvals")
for tr in ['645', '1400', '2500']:
dcm2nii_others = pe.Node(DcmStack(), name="dcm2nii_%s" % tr)
dcm2nii_others.inputs.embed_meta = True
dcm2nii_others.plugin_args = {'submit_specs': 'request_memory = 2000'}
wf.connect(datagrabber, tr, dcm2nii_others, "dicom_files")
others_rename = pe.Node(util.Rename(), name="others_rename%s" % tr)
others_rename.inputs.format_string = {
'645': 'RfMRI_mx_645.nii.gz',
'1400': 'RfMRI_mx_1400.nii.gz',
'2500': 'RfMRI_std_2500.nii.gz'
}[tr]
wf.connect(dcm2nii_others, "out_file", others_rename, "in_file")
ds = pe.Node(nio.DataSink(), name="datasink%s" % tr)
ds.inputs.base_directory = '/scr/kalifornien1/data/nki_enhanced/'
ds.inputs.substitutions = [('_subject_id_', '')]
def create_converter_functional_pipeline(working_dir,
ds_dir,
name='converter_funct'):
# initiate workflow
converter_wf = Workflow(name=name)
converter_wf.base_dir = os.path.join(working_dir, 'LeiCA_resting')
# set fsl output
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# I/O NODE
inputnode = Node(
util.IdentityInterface(fields=['epi_dicom', 'out_format']),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=['epi', 'TR_ms']),
name='outputnode')
niftisink = Node(nio.DataSink(), name='niftisink')
niftisink.inputs.base_directory = os.path.join(ds_dir, 'raw_niftis')
niftisink.inputs.substitutions = [('_TR_id_', 'TR_')]
# convert to nifti
# todo check if geometry bugs attac. use dcm2nii?
converter_epi = Node(DcmStack(embed_meta=True), name='converter_epi')
converter_epi.plugin_args = {'submit_specs': 'request_memory = 2000'}
def reformat_filename_fct(TR_str):
return 'rsfMRI_' + TR_str
reformat_filename = Node(util.Function(input_names=['TR_str'],
output_names=['filename'],
function=reformat_filename_fct),
name='reformat_filename')
converter_wf.connect(inputnode, 'out_format', reformat_filename, 'TR_str')
converter_wf.connect(inputnode, 'epi_dicom', converter_epi, 'dicom_files')
converter_wf.connect(reformat_filename, 'filename', converter_epi,
'out_format')
# reorient to standard orientation
reor_2_std = Node(fsl.Reorient2Std(), name='reor_2_std')
converter_wf.connect(converter_epi, 'out_file', reor_2_std, 'in_file')
converter_wf.connect(reor_2_std, 'out_file', outputnode, 'epi')
# save original niftis
converter_wf.connect(reor_2_std, 'out_file', niftisink, 'rsfMRI')
# GET TR FROM .nii
def check_TR_fct(TR):
print ' '
print 'check_TR_fct checks validity of TR'
print('imported TR is %s' % TR)
print ' '
try:
float(TR)
except ValueError:
isvalid_TR = 0
raise Exception(
'ERROR: TR COULD NOT AUTOMATICALLY BE EXTRACTED FROM EPI.\nEXECUTION STOPPED'
)
else:
isvalid_TR = 1
print 'TR is valid'
if isvalid_TR:
if float(TR <= 0):
raise Exception(
'ERROR: TR NOT VALID (<=0).\nEXECUTION STOPPED')
return float(TR)
get_TR = Node(ImageInfo(), name='get_TR')
converter_wf.connect(reor_2_std, 'out_file', get_TR, 'in_file')
check_TR = Node(util.Function(input_names=['TR'],
output_names=['TR_ms'],
function=check_TR_fct),
name='check_TR')
converter_wf.connect(get_TR, 'TR', check_TR, 'TR')
converter_wf.connect(check_TR, 'TR_ms', outputnode, 'TR_ms')
converter_wf.write_graph(dotfilename=converter_wf.name,
graph2use='flat',
format='pdf')
return converter_wf
t1s_gunzip = pe.Node(util.Function(input_names=['file'],
output_names=['dir'],
function=gunzip),
name="t1s_gunzip")
wf.connect(datagrabber, "t1s", t1s_gunzip, "file")
resting_gunzip = pe.Node(util.Function(input_names=['file'],
output_names=['dir'],
function=gunzip),
name="resting_gunzip")
wf.connect(datagrabber, "resting", resting_gunzip, "file")
# dcm2nii_t1s = pe.Node(DcmStack(), name="dcm2nii_t1s")
# dcm2nii_t1s.inputs.embed_meta = True
# wf.connect(t1s_gunzip, "dir", dcm2nii_t1s, "dicom_files")
dcm2nii_resting = pe.Node(DcmStack(), name="dcm2nii_resting")
dcm2nii_resting.inputs.embed_meta = True
def add_asterix(s):
return s + "/*"
wf.connect(resting_gunzip, ("dir", add_asterix), dcm2nii_resting,
"dicom_files")
# recon_all = pe.Node(ReconAll(), name="recon_all")
# #recon_all.inputs.subjects_dir = "/scr/adenauer1/freesurfer"
# wf.connect(dcm2nii_t1s, "out_file", recon_all, "T1_files")
# wf.connect(subjects_infosource, "subject_id", recon_all, "subject_id")
wf.run(plugin="Linear")