def check_fsl(version_requirements=None):
"""Check FSL software."""
import nipype.interfaces.fsl as fsl
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
from clinica.utils.stream import cprint
check_environment_variable("FSLDIR", "FSL")
try:
if fsl.Info.version().split(".") < ["5", "0", "5"]:
raise ClinicaMissingDependencyError(
f"{Fore.RED}FSL version must be greater than 5.0.5{Fore.RESET}"
)
except Exception as e:
cprint(str(e))
list_binaries = ["bet", "flirt", "fast", "first"]
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
f"{Fore.RED}\n[Error] Clinica could not find FSL software: "
f"the {binary} command is not present in your PATH environment.{Fore.RESET}"
)
def check_environment_variable(environment_variable, software_name):
import os
content_var = os.environ.get(environment_variable, "")
if not content_var:
raise ClinicaMissingDependencyError(
f"Clinica could not find {software_name} software: "
f"the {environment_variable} variable is not set.")
if not os.path.isdir(content_var):
raise ClinicaMissingDependencyError(
f"The {environment_variable} environment variable "
f"you gave is not a folder (content: {content_var}).")
return content_var
def check_environment_variable(environment_variable, software_name):
import os
from colorama import Fore
from .exceptions import ClinicaMissingDependencyError
content_var = os.environ.get(environment_variable, '')
if not content_var:
raise ClinicaMissingDependencyError(
'%s\n[Error] Clinica could not find %s software: the %s variable is not set.%s'
% (Fore.RED, software_name, environment_variable, Fore.RESET))
if not os.path.isdir(content_var):
raise ClinicaMissingDependencyError(
'%s\n[Error] The %s environment variable you gave is not a folder (content: %s).%s'
% (Fore.RED, environment_variable, content_var, Fore.RESET))
return content_var
def check_petpvc(version_requirements=None):
"""Check PETPVC software."""
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
list_binaries = [
"petpvc",
"pvc_diy",
"pvc_gtm",
"pvc_iy",
"pvc_labbe",
"pvc_make4d",
"pvc_mg",
"pvc_mtc",
"pvc_rbv",
"pvc_relabel",
"pvc_rl",
"pvc_simulate",
"pvc_stc",
"pvc_vc",
]
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
f"{Fore.RED}\n[Error] Clinica could not find PETPVC software: the "
f"{binary} command is not present in your PATH environment.{Fore.RESET}"
)
def check_dcm2niix():
"""Check dcm2niix software."""
if not is_binary_present("dcm2niix"):
raise ClinicaMissingDependencyError(
"Clinica could not find dcm2niix software in your PATH environment: "
"this can be downloaded or installed from https://github.com/rordenlab/dcm2niix."
)
def check_convert3d(version_requirements=None):
"""Check Convert3D software."""
list_binaries = ["c3d_affine_tool", "c3d"]
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
f"[Error] Clinica could not find Convert3D software: "
f"the {binary} command is not present in your PATH environment."
)
def check_matlab():
"""Check Matlab toolbox."""
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
if not is_binary_present("matlab"):
raise ClinicaMissingDependencyError(
'%sMatlab was not found in PATH environment. Did you add it?%s' %
(Fore.RED, Fore.RESET))
def check_environment_variable(environment_variable, software_name):
import os
from colorama import Fore
from .exceptions import ClinicaMissingDependencyError
content_var = os.environ.get(environment_variable, "")
if not content_var:
raise ClinicaMissingDependencyError(
f"{Fore.RED}\n[Error] Clinica could not find {software_name} software: "
f"the {environment_variable} variable is not set.{Fore.RESET}"
)
if not os.path.isdir(content_var):
raise ClinicaMissingDependencyError(
f"{Fore.RED}\n[Error] The {environment_variable} environment variable "
f"you gave is not a folder (content: {content_var}).{Fore.RESET}"
)
return content_var
def check_dcm2niix():
"""Check dcm2niix software."""
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
if not is_binary_present('dcm2niix'):
raise ClinicaMissingDependencyError(
'%s\n[Error] Clinica could not find dcm2niix software in your PATH environment: '
'this can be downloaded or installed from https://github.com/rordenlab/dcm2niix.%s' %
(Fore.RED, Fore.RESET))
def check_dcm2nii():
"""Check dcm2nii software."""
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
if not is_binary_present('dcm2nii'):
raise ClinicaMissingDependencyError(
'%s\n[Error] Clinica could not find dcm2nii tool from MRIcron in your PATH environment: '
'this can be downloaded from https://www.nitrc.org/frs/?group_id=152 (choose the 2016 version).%s' %
(Fore.RED, Fore.RESET))
def check_ants(version_requirements=None):
"""Check ANTs software."""
check_environment_variable("ANTSPATH", "ANTs")
list_binaries = ["N4BiasFieldCorrection", "antsRegistrationSyNQuick.sh"]
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
"Clinica could not find ANTs software: "
f"the {binary} command is not present in your PATH environment."
)
def check_custom_dependencies(self):
"""Check dependencies that can not be listed in the `info.json` file."""
from clinica.utils.check_dependency import is_binary_present
from clinica.utils.exceptions import ClinicaMissingDependencyError
if self.parameters["use_cuda"]:
if not is_binary_present("eddy_cuda"):
raise ClinicaMissingDependencyError(
"[Error] FSL eddy with CUDA was set but Clinica could not find eddy_cuda in your PATH environment. "
"Check that https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide#The_eddy_executables is correctly set."
)
def check_petpvc(version_requirements=None):
"""Check PETPVC software."""
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
list_binaries = ['petpvc', 'pvc_diy', 'pvc_gtm', 'pvc_iy', 'pvc_labbe', 'pvc_make4d', 'pvc_mg',
'pvc_mtc', 'pvc_rbv', 'pvc_relabel', 'pvc_rl', 'pvc_simulate', 'pvc_stc', 'pvc_vc']
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
'%s\n[Error] Clinica could not find PETPVC software: the %s command is not present in your '
'PATH environment.%s' % (Fore.RED, binary, Fore.RESET))
def check_freesurfer(version_requirements=None):
"""Check FreeSurfer software."""
check_environment_variable("FREESURFER_HOME", "FreeSurfer")
list_binaries = ["mri_convert", "recon-all"]
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
"Clinica could not find FreeSurfer software: "
f"the {binary} command is not present in your PATH environment: "
"did you have the line `source $FREESURFER_HOME/SetUpFreeSurfer.sh` "
"in your configuration file?")
def check_mrtrix(version_requirements=None):
"""Check MRtrix software."""
from clinica.utils.exceptions import ClinicaMissingDependencyError
list_binaries = [
"transformconvert", "mrtransform", "dwi2response", "tckgen"
]
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
f"Clinica could not find MRtrix software: "
f"the {binary} command is not present in your PATH environment."
)
def check_mrtrix(version_requirements=None):
"""Check MRtrix software."""
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
check_environment_variable('MRTRIX_HOME', 'MRtrix')
list_binaries = ['transformconvert', 'mrtransform', 'dwi2response', 'tckgen']
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
'%s\n[Error] Clinica could not find MRtrix software: the %s command is not present in your '
'PATH environment.%s' % (Fore.RED, binary, Fore.RESET))
def check_ants(version_requirements=None):
"""Check ANTs software."""
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
check_environment_variable('ANTSPATH', 'ANTs')
list_binaries = ['N4BiasFieldCorrection', 'antsRegistrationSyNQuick.sh']
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
'%s\n[Error] Clinica could not find ANTs software: the %s command is not present '
'in your PATH environment.%s' % (Fore.RED, binary, Fore.RESET))
def check_fsl(version_requirements=None):
"""Check FSL software."""
import nipype.interfaces.fsl as fsl
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
from clinica.utils.stream import cprint
check_environment_variable('FSLDIR', 'FSL')
try:
if fsl.Info.version().split(".") < ['5', '0', '5']:
raise ClinicaMissingDependencyError(
'%sFSL version must be greater than 5.0.5%s' %
(Fore.RED, Fore.RESET))
except Exception as e:
cprint(str(e))
list_binaries = ['bet', 'flirt', 'fast', 'first']
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
'%s\n[Error] Clinica could not find FSL software: the %s command is not present in your '
'PATH environment.%s' % (Fore.RED, binary, Fore.RESET))
def check_freesurfer(version_requirements=None):
"""Check FreeSurfer software."""
from colorama import Fore
import nipype.interfaces.freesurfer as freesurfer
from clinica.utils.exceptions import ClinicaMissingDependencyError
check_environment_variable('FREESURFER_HOME', 'FreeSurfer')
list_binaries = ['mri_convert', 'recon-all']
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
'%s\n[Error] Clinica could not find FreeSurfer software: the %s command is not present in your PATH '
'environment: did you have the line source ${FREESURFER_HOME}/'
'SetUpFreeSurfer.sh in your configuration file?%s' % (Fore.RED, binary, Fore.RESET))
def check_mrtrix(version_requirements=None):
"""Check MRtrix software."""
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
check_environment_variable("MRTRIX_HOME", "MRtrix")
list_binaries = ["transformconvert", "mrtransform", "dwi2response", "tckgen"]
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
f"{Fore.RED}\n[Error] Clinica could not find MRtrix software: "
f"the {binary} command is not present in your PATH environment.{Fore.RESET}"
)
def check_ants(version_requirements=None):
"""Check ANTs software."""
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
check_environment_variable("ANTSPATH", "ANTs")
list_binaries = ["N4BiasFieldCorrection", "antsRegistrationSyNQuick.sh"]
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
f"{Fore.RED}\n[Error] Clinica could not find ANTs software: "
f"the {binary} command is not present in your PATH environment.{Fore.RESET}"
)
def check_software_requirements(current_version, version_requirements, software_name):
from distutils.version import LooseVersion
from string import punctuation
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
comparison_operator = ''.join([c for c in version_requirements if c in punctuation.replace('.', '')])
required_version = version_requirements.replace(comparison_operator, '')
satisfy_version = eval('LooseVersion(\'%s\') %s LooseVersion(\'%s\')' %
(current_version, comparison_operator, required_version))
if not satisfy_version:
raise ClinicaMissingDependencyError(
'%s\n[Error] Your %s version (%s) does not version requirements (%s).%s' %
(Fore.RED, software_name, current_version, version_requirements, Fore.RESET))
def check_software_requirements(current_version, version_requirements,
software_name):
from string import punctuation
comparison_operator = "".join(
[c for c in version_requirements if c in punctuation.replace(".", "")])
required_version = version_requirements.replace(comparison_operator, "")
satisfy_version = eval(
f"LooseVersion('{current_version}') {comparison_operator} LooseVersion('{required_version}')"
)
if not satisfy_version:
raise ClinicaMissingDependencyError(
f"Your {software_name} version ({current_version}) "
f"does not satisfy version requirements ({version_requirements}).")
def check_cat12():
"""
Check installation of CAT12 (mostly used to provide atlases)
"""
import os
from colorama import Fore
from .exceptions import ClinicaMissingDependencyError
from .spm import check_spm_home
spm_home = check_spm_home()
cat12 = os.path.join(spm_home, 'toolbox', 'cat12')
if not os.path.exists(cat12):
raise ClinicaMissingDependencyError(
'%s\n[Error] CAT12 is not installed in your SPM folder. It should be in %s.%s'
% (Fore.RED, cat12, Fore.RESET))
return cat12
def check_freesurfer(version_requirements=None):
"""Check FreeSurfer software."""
import nipype.interfaces.freesurfer as freesurfer
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
check_environment_variable("FREESURFER_HOME", "FreeSurfer")
list_binaries = ["mri_convert", "recon-all"]
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
f"{Fore.RED}\n[Error] Clinica could not find FreeSurfer software: "
f"the {binary} command is not present in your PATH environment: "
f"did you have the line source ${{FREESURFER_HOME}}/SetUpFreeSurfer.sh "
f"in your configuration file?{Fore.RESET}"
)
def check_software_requirements(current_version, version_requirements, software_name):
from string import punctuation
from colorama import Fore
from clinica.utils.exceptions import ClinicaMissingDependencyError
comparison_operator = "".join(
[c for c in version_requirements if c in punctuation.replace(".", "")]
)
required_version = version_requirements.replace(comparison_operator, "")
satisfy_version = eval(
f"LooseVersion('{current_version}') {comparison_operator} LooseVersion('{required_version}')"
)
if not satisfy_version:
raise ClinicaMissingDependencyError(
f"{Fore.RED}\n[Error] Your {software_name} version ({current_version}) "
f"does not satisfy version requirements ({version_requirements}).{Fore.RESET}"
)
def run_command(self, args):
from os.path import exists
from os import makedirs
from colorama import Fore
from clinica.iotools.converters.aibl_to_bids.aibl_to_bids import convert_clinical_data, convert_images
from clinica.utils.check_dependency import is_binary_present, check_freesurfer
from clinica.utils.exceptions import ClinicaMissingDependencyError
list_binaries = ['dcm2niix', 'dcm2nii']
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
'%s\n[Error] Clinica could not find %s software: it is not present in your '
'PATH environment.%s' % (Fore.RED, binary, Fore.RESET))
check_freesurfer()
if not exists(args.bids_directory):
makedirs(args.bids_directory)
convert_images(args.dataset_directory, args.clinical_data_directory,
args.bids_directory)
convert_clinical_data(args.bids_directory,
args.clinical_data_directory)
def check_petpvc(version_requirements=None):
"""Check PETPVC software."""
list_binaries = [
"petpvc",
"pvc_diy",
"pvc_gtm",
"pvc_iy",
"pvc_labbe",
"pvc_make4d",
"pvc_mg",
"pvc_mtc",
"pvc_rbv",
"pvc_relabel",
"pvc_rl",
"pvc_simulate",
"pvc_stc",
"pvc_vc",
]
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
"Clinica could not find PETPVC software: "
f"the {binary} command is not present in your PATH environment."
)
def check_matlab():
"""Check Matlab toolbox."""
if not is_binary_present("matlab"):
raise ClinicaMissingDependencyError(
"Matlab was not found in PATH environment. Did you add it?")