def RegisterCT2MRI():
text = "Runs registration of CT imaging (moving) and T1-sequence (fixed) in order to get them into same space. " \
"The default option (see cfg-file) constitutes three steps: a) Rigid, b) Affine registration and c) " \
"Symmetric image Normalisation (SyN). For details see 'SyNRA'-option at " \
"https://github.com/ANTsX/ANTsPy/blob/master/ants/registration/interface.py. Non-default means, that the " \
"command-line for running ANTsRegistration can be modified according to the file: " \
"cmdline_ANTsRegistration.txt in the .utils directory. Please make sure to include all terms within *...* " \
"into the text-file as they will be replaced."
return Output.split_lines(text)
def RegisterMRI2template():
text = "Runs registration of MR-imaging (moving) to template sequences (fixed) as defined in the config file in " \
"order to get them into same space. The default option constitutes three steps: a) Rigid, " \
"b) Affine registration and c) Symmetric image Normalisation (SyN), although all options available in ANTsPy" \
"are possible (for details see https://github.com/ANTsX/ANTsPy/blob/master/ants/registration/interface.py. " \
"Non-default means, that the command-line for running ANTsRegistration can be modified according to " \
"the file: cmdline_ANTsRegistration.txt in the .utils directory. Please make sure to include all terms " \
"within *...* into the text-file as they will be replaced."
return Output.split_lines(text)
def wrapper_multiprocessing(self, fileIDs, subjects, modality):
"""To avoid redundancy between CT and MR registration to common space, this part is wrapped up here """
working_dir = self.cfg['folders']['nifti']
prefix = '{}2template'.format(modality)
# Start multiprocessing framework
start_multi = time.time()
status = mp.Queue()
processes = [
mp.Process(target=self.ANTsCoregisterMultiprocessing,
args=(filename_fixed, filename_moving, no_subj,
os.path.join(working_dir, no_subj),
'registration', prefix, status))
for filename_fixed, filename_moving, no_subj in fileIDs
]
for p in processes:
p.start()
while any([p.is_alive() for p in processes]):
while not status.empty():
filename_fixed, filename_moving, no_subj = status.get()
print("\tRegistering {} (f) to {} (m), in ANTsPy\n".format(
filename_fixed,
os.path.split(filename_moving)[1], no_subj))
time.sleep(0.1)
for p in processes:
p.join()
# Functions creating/updating pipeline log, which documents all steps along with settings
for subjID in subjects:
files_processed = [(os.path.split(file_moving)[1],
os.path.split(file_fixed)[1])
for file_fixed, file_moving, subj_no in fileIDs
if subj_no == subjID]
log_text = "{} successfully registered (@{}) to \n{}, \n\n Mean Duration per subject: {:.2f} " \
"secs".format(files_processed[0][0], time.strftime("%Y%m%d-%H%M%S"), files_processed[0][1],
(time.time() - start_multi) / len(subjects))
Output.logging_routine(text=Output.split_lines(log_text),
cfg=self.cfg,
subject=str(subjID),
module='{}-Registration'.format(modality),
opt=self.cfg['preprocess']['registration'],
project="")
print(
'\nIn total, a list of {} subject(s) was processed; {} registration took {:.2f}secs. '
'overall'.format(len(subjects), modality,
time.time() - start_multi))
def LabelFilenameDCM2NII():
text = "Please enter here the prefix/file information that should be included when saving NIFTI files. " \
"Characters such as '<', '>', ':', '/' ... MUST be avoided (default is %p_%s). " \
"From documentation:\n\t %a : antenna (coil) number inserted. For example, the output filename" \
" 'myName%a' would generate 'myName1', 'myName2', each for each coil. Note that most scans combine data " \
"from all coils and in these cases this option is ignored. For example, most scans which combine " \
"data from all coils would simply be called 'myName'\n\t%d :" \
"series description (0008,103E) inserted. For example, an echo-planar image " \
"converted with 'myName%d' would yield 'myNameEPI' \n\t%e : echo number " \
"inserted. For example, a sequence with two echo times converted with the output" \
"filename 'myName%e' will yield 'myName1' and 'myName2'. Note that most MRI" \
" sequences only use a single echo time, and in these cases you would only get " \
"'myName1'.\n\t%f : input folder name inserted. For example, the output " \
"filename'myName%f' combined with an input folder '/usr/Subj22' will result in " \
"the output file named'myNameSubj22.nii' \n\t%i : patient ID " \
"(DICOM tag 0010,0020) inserted. For example, the output filename 'myName%i' " \
" would convert an image where the patient ID is named 'ID123' to be " \
" 'myNameID123.nii' \n\t%m : manufacturer name For example, the output filename" \
" 'myName%m' would convert an image from a GE scanner to 'myNameGE.nii', while " \
" an image from Philips would be 'myNamePh.nii', whereas Siemens would be " \
" 'myNameSi.nii', otherwise the manufacturer is not available ('myNameNA.nii')." \
" (requires dcm2nii versions from 2015 or later). \n\t%n : subject name (DICOM" \
" tag 0010,0010) inserted. For example, the output filename 'myName%n' would " \
" convert an image from John Doe to 'myNameJohnDoe.nii'. This option works best" \
" if your participant names use only English letters, for other European " \
" languages you may find it makes some basic conversions ('Müller' will become " \
" 'Muller'). For non-European languages you will find this option unsatisfactory" \
". Perhaps future versions can support DICOM tag 0008,0005. \n\t %p: protocol" \
" name (DICOM tag 0018,1030) inserted. For example, the output filename" \
" 'myName%p' would convert image where protocol is named T1 to be 'myNameT1.nii'" \
" \n\t%q: sequence name (DICOM tag 0018,1020) inserted.For example," \
" the output filename 'myName%q' would convert a Spin Echo sequence to be " \
"'myNameSE.nii' (new feature, in versions from 30Aug2015).\n\t%s : series (DICOM " \
"tag 0020,0011) inserted. For example, the output filename 'myName%s' would " \
"convert the second series to be 'myName2.nii'. If you want to zero-pad the " \
"series number, insert the number of digits desired (0..9). For example applying " \
"the filter 'm%s' when converting 11 series will create files that will cause" \
" problems for a simple alphabetical sort, e.g. 'm1.nii,m11.nii,m2.nii...m9.nii'." \
" In contrast specifying 'm%3s' will help sorting (e.g. 'm001.nii,m002.nii" \
"...m011.nii').\n\t%t : session date and time inserted (DICOM tags 0008,0021 and " \
"0008,0030). For example, the output filename 'myName%t' would convert an image " \
"where the session began at 1:23pm on 13 Jan 2014 as 'myName20140113132322.nii' " \
"\n\t%z : Sequence Name (0018,0024) inserted, so a T1 scan converted with " \
"'myName%z' might yield 'myNameT1'."
return Output.split_lines(text)
def renameFolders():
text = 'Displays a small GUI which enables to change the prefix for all folders. This new prefix is saved in ' \
'the configuration file'
return Output.split_lines(text)
def ProbabilisticMask():
text = 'Defines whether or not use probablisitic mask. With the use of ANTs for registration and segmentation, ' \
' a probabilistic mask is created via ANTsPyNet routines. if set to "yes", the 95th percentile is used, ' \
' otherwise data is subtracted from the edges with a sphere analog to the procedure in Lead-DBS'
return Output.split_lines(text)
def dcm2niix_multiprocessing(self, name_subj, no_subj, dcm2niix_bin,
last_idx, total_subj, status):
"""function intended to provide multiprocessing approach to speed up extraction of DICOM data to nifti files"""
modalities = ['CT', 'MRI']
if self.logfile:
log_filename = os.path.join(
ROOTDIR, 'logs', 'log_DCM2NII_' + str(no_subj + last_idx) +
time.strftime("%Y%m%d-%H%M%S"))
else:
log_filename = os.devnull
subj_outdir = os.path.join(
self.outdir,
self.cfg['folders']['prefix'] + str(no_subj + last_idx))
FileOperations.create_folder(subj_outdir)
start_time_subject = time.time()
keptfiles, deletedfiles = ([] for _ in range(2))
for mod in modalities:
status.put((name_subj, mod, no_subj, total_subj))
input_folder_name = os.path.join(self.inputdir, name_subj + mod)
# input_folder_files = [f.path for f in os.scandir(input_folder_name)
# if (f.is_dir() and ('100' in f.path or 'DICOM' in f.path or '001' in f.path))]
input_folder_files = []
[
input_folder_files.append(item)
for item in os.listdir(input_folder_name)
if (os.path.isdir(os.path.join(input_folder_name, item)) and (
'100' in item or 'DICOM' in item or '001' in item))
]
orig_stdout = sys.stdout
sys.stdout = open(log_filename, 'w')
for folder in input_folder_files:
subprocess.call(
[
dcm2niix_bin,
'-a',
'y', # anonimisation of DICOM data
'-b',
self.cfg['preprocess']['dcm2nii']['BIDSsidecar'][0],
'-z',
self.cfg['preprocess']['dcm2nii']['OutputCompression']
[0],
'-f',
self.cfg['preprocess']['dcm2nii']['OutputFileStruct'],
'-o',
subj_outdir,
'-w',
str(self.cfg['preprocess']['dcm2nii']
['NameConflicts']),
'-v',
str(self.cfg['preprocess']['dcm2nii']['Verbosity']),
'-x',
str(self.cfg['preprocess']['dcm2nii']['ReorientCrop']),
folder
],
stdout=sys.stdout,
stderr=subprocess.STDOUT)
sys.stdout.close()
sys.stdout = orig_stdout
files_kept, files_deleted = self.select_sequences(subj_outdir)
keptfiles.extend(files_kept)
deletedfiles.extend(files_deleted)
# Functions creating/updating pipeline log, which document individually all steps along with settings
log_text = "{} files successfully converted: {}, \n\nand {} deleted: {}.\nDuration: {:.2f} secs" \
.format(len(set(keptfiles)),
'\n\t{}'.format('\n\t'.join(os.path.split(x)[1] for x in sorted(set(keptfiles)))),
len(set(deletedfiles)),
'\n\t{}'.format('\n\t'.join(os.path.split(x)[1] for x in sorted(set(deletedfiles)))),
time.time() - start_time_subject)
Output.logging_routine(text=Output.split_lines(log_text),
cfg=self.cfg,
subject=self.cfg['folders']['prefix'] +
str(no_subj),
module='dcm2nii',
opt=self.cfg['preprocess']['dcm2nii'],
project="")
def runDCM2NII():
text = 'Separate GUI to transform DICOM files using Chris Rordens routines ' \
'see http://www.nitrc.org/projects/dcm2nii/'
return Output.split_lines(text)
def LabelVerbosity():
text = "According to the documentation this defines whether dcm2nii should be silent (0), with numerous" \
" output (1) or logorrhoeic (2); default = 1"
return Output.split_lines(text)
def LabelResampleImages():
text = "Defines the spacing to which imaging will be resampled at. If set to '0' resampling is skipped"
return Output.split_lines(text)
def N4BiasCorrection():
text = "Reduces the Bias from the MRI using the N4Bias correction method as described in N.J. Tustison, ..., and " \
"J.C. Gee. "'N4ITK: Improved N3 Bias Correction IEEE Transactions on Medical Imaging, ' \
"29(6):1310-1320, June 2010."
return Output.split_lines(text)
def BSplineDistance():
text = "B-spline fitting parameters. With respect to the official documentation, only sizing of the mesh " \
"elements can be used, whereas the other possible options are left as default. A float value of " \
"the distance between the knots defining the B-Spline mesh can be chosen"
return Output.split_lines(text)
def displayFolderContent():
text = 'Display the data available for the subj selected, to see what is present. Note: if more than one ' \
'subject is selected an error will be dropped!'
return Output.split_lines(text)
def LabelShrink():
text = "Downsample level applied, specified as integer (factors <= 4 commonly used, see https://manpages.ubuntu.com/manpages/trusty/man1/N4BiasFieldCorrection.1.html)."
return Output.split_lines(text)
def LabelPrefixBias():
text = "The prefix for the N4Bias-corrected files. Be cautious here as changing this may result in some parts of the toolbox not working"
return Output.split_lines(text)
def LabelReorientCrop():
text = "This option sets whether reorientation according to header and cropping should be performed or not"
return Output.split_lines(text)
def renameFoldersInput():
text = "Please enter here the string that replaces the suffix (see left). \nIt may only contain characters, " \
"numbers and the special characters: '_' and '.', but not at the end "
return Output.split_lines(text)
def ResampleMethod():
text = "Defines the method appled for resampling images: \n\t - (lin) - linear\n\t - (nn) - nearest neighbour\n\t - (gauss) - gaussian \n\t - (bspline) - B-spline interpolation"
return Output.split_lines(text)
def subjectDetails():
text = 'Displays the subject details and the names of the subjects corresponding to the prefix'
return Output.split_lines(text)
def compareNIFTIfiles():
text = "Opens a dialog in order to select NIFTI-files which can be displayed using the image viewer. This enables" \
" to see whether there have been any problems whatsoever"
return Output.split_lines(text)
def ANTsSettings():
text = "Displays a separate window in which the options for the ANTsPy routines can be modified."
return Output.split_lines(text)
def saveDirButton():
text = "The folder is saved into a configuration file, which is read when GUI is loaded in order to " \
"facilitate continuing with previous session (file located in main folder of Toolbox). Only available " \
"for some parts of the code"
return Output.split_lines(text)
def N4BiasConvergence():
text = "Maximum number of iterations for each shrinkage factor and convergence tolerance"
return Output.split_lines(text)
def LabelBIDS():
text = "This option sets whether sidecar is stored or not (By default, data is always anonimised and BIDS " \
"are always stored). "
return Output.split_lines(text)
def ChangeWdirDICOM():
text = (
'Opens another dialog in which the DICOM directory may be changed. For actions to take place, press '
'"reload files" button')
return Output.split_lines(text)
def DiffPrefix():
text = "Prefix for diffusion weighted imaging sequences (if available)."
return Output.split_lines(text)
def run_dcm2niix():
text = "Before running this script, please make sure that the prefrences are set properly. moreover it is " \
"recommended to name DICOM folders xxxCT and xxxMRI or one of both. cDBS will specifically look for these " \
"folders to convert DICOM data from."
return Output.split_lines(text)
def PaCER_MetalThreshold():
text = "The threshold used to scan for artifacts which may correspond to a lead within the mask of the brain. " \
"In case none is found, this is lowered automatically"
return Output.split_lines(text)
def __init__(self, parent=None):
super(QWidget, self).__init__(parent)
# Load configuration files and general settings
self.cfg = Configuration.load_config(ROOTDIR)
if os.path.isdir(self.cfg['folders']['dicom']):
self.dicomdir = self.cfg['folders']['dicom']
else:
self.dicomdir = FileOperations.set_wdir_in_config(self.cfg, foldername='dicom', init=True)
self.cfg['folders']['dicom'] = self.dicomdir
self.cfg['folders']['rootdir'] = ROOTDIR
Configuration.save_config(ROOTDIR, self.cfg)
# Create general layout
self.tot_layout = QVBoxLayout(self)
self.mid_layout = QHBoxLayout(self)
# ============================ Create upper of GUI, i.e. working directory ============================
self.folderboxDcm2nii = QGroupBox("Directory (DICOM-files)")
self.HBoxUpperDcm2nii = QVBoxLayout(self.folderboxDcm2nii)
self.label_dicomdir = QLabel('dicom DIR: {}'.format(self.dicomdir))
self.HBoxUpperDcm2nii.addWidget(self.label_dicomdir)
self.btn_dicomdir = QPushButton('Change working \ndirectory')
self.btn_dicomdir.setFixedSize(150, 40)
self.btn_dicomdir.clicked.connect(self.change_dicomdir)
self.btn_savedir = QPushButton('Save directory \nto config file')
self.btn_savedir.setFixedSize(150, 40)
self.btn_savedir.setToolTip(Output.split_lines(setToolTips.saveDirButton()))
self.btn_savedir.clicked.connect(self.save_cfg)
hlay_upper = QHBoxLayout()
hlay_upper.addWidget(self.btn_dicomdir)
hlay_upper.addWidget(self.btn_savedir)
hlay_upper.addStretch(1)
self.HBoxUpperDcm2nii.addLayout(hlay_upper)
# ==================== Create Content for Lists, i.e. input/output ====================
self.listboxInputDcm2nii = QGroupBox('Available subjects in working directory')
self.listboxInput = QVBoxLayout(self.listboxInputDcm2nii)
self.mInput = QListWidget()
self.listboxInput.addWidget(self.mInput)
self.mButtonToAvailable = QPushButton("<<")
self.mBtnMoveToAvailable = QPushButton(">")
self.mBtnMoveToSelected = QPushButton("<")
self.mButtonToSelected = QPushButton(">>")
self.mBtnUp = QPushButton("Up")
self.mBtnDown = QPushButton("Down")
self.listboxOutputDcm2nii = QGroupBox('Subjects to process')
self.listboxOutput = QVBoxLayout(self.listboxOutputDcm2nii)
self.mOutput = QListWidget()
self.listboxOutput.addWidget(self.mOutput)
# First column on the left side
vlay = QVBoxLayout()
vlay.addStretch()
vlay.addWidget(self.mBtnMoveToAvailable)
vlay.addWidget(self.mBtnMoveToSelected)
vlay.addStretch()
vlay.addWidget(self.mButtonToAvailable)
vlay.addWidget(self.mButtonToSelected)
vlay.addStretch()
# Second column on the right side
vlay2 = QVBoxLayout()
vlay2.addStretch()
vlay2.addWidget(self.mBtnUp)
vlay2.addWidget(self.mBtnDown)
vlay2.addStretch()
# ==================== Lower part of GUI, i.e. Preferences/Start estimation ====================
self.btn_preferences = QPushButton("Preferences")
self.btn_preferences.clicked.connect(self.settings_show)
self.btn_run_dcm2niix = QPushButton("Run dcm2niix")
self.btn_run_dcm2niix.setToolTip(setToolTips.run_dcm2niix())
self.btn_run_dcm2niix.clicked.connect(self.start_converting)
hlay_bottom = QHBoxLayout()
hlay_bottom.addStretch(1)
hlay_bottom.addWidget(self.btn_preferences)
hlay_bottom.addWidget(self.btn_run_dcm2niix)
hlay_bottom.addStretch()
# ==================== Set all contents to general Layout =======================
self.mid_layout.addWidget(self.listboxInputDcm2nii)
self.mid_layout.addLayout(vlay)
self.mid_layout.addWidget(self.listboxOutputDcm2nii)
self.mid_layout.addLayout(vlay2)
self.tot_layout.addWidget(self.folderboxDcm2nii)
self.tot_layout.addLayout(self.mid_layout)
self.tot_layout.addLayout(hlay_bottom)
try:
self.mInput.clear()
items = FileOperations.list_folders(inputdir=self.cfg['folders']['dicom'], prefix='', files2lookfor='')
items = self.check_for_complete_input(list(items))
self.add_available_subj(items)
except FileExistsError:
print('{} without any valid files/folders, continuing ...'.format(self.dicomdir))
self.update_buttons_status()
self.connections()
def PaCER_Lambda():
text = "Not sure what it does!! Please double check"
return Output.split_lines(text)