def _environment(self):
""" Return a dictionary of the environment needed by FreeSurfer
binaries.
"""
# Check if FreeSurfer has already been configures
env = os.environ.get("FREESURFER_CONFIGURED", None)
# Configure FreeSurfer
if env is None:
# FreeSurfer home directory
fs_home = os.environ.get("FREESURFER_HOME", None)
env = {}
if fs_home is not None:
env["FREESURFER_HOME"] = fs_home
# Parse configuration file
env = environment(self.shfile, env)
# Save the result
os.environ["FREESURFER_CONFIGURED"] = json.dumps(env)
# Load configuration
else:
env = json.loads(env)
return env
def _environment(self):
""" Return a dictionary of the environment needed by FreeSurfer
binaries.
"""
# Check if FreeSurfer has already been configures
env = os.environ.get("FREESURFER_CONFIGURED", None)
# Configure FreeSurfer
if env is None:
# FreeSurfer home directory
fs_home = os.environ.get("FREESURFER_HOME", None)
env = {}
if fs_home is not None:
env["FREESURFER_HOME"] = fs_home
# Parse configuration file
env = environment(self.shfile, env)
# Save the result
os.environ["FREESURFER_CONFIGURED"] = json.dumps(env)
# Load configuration
else:
env = json.loads(env)
return env
def run_freesurfer_cmd(cmd, subjects_dir=None, add_fsl_env=False,
fsl_init="/etc/fsl/5.0/fsl.sh"):
"""
To avoid repeating the code to run Freesurfer and check exitcode
everywhere.
Step:
- add $SUBJECTS_DIR to the environment if requested
- add FSL's environment if requested (some Freesurfer commands require
FSL)
- run the Freesurfer cmd
- check exit code
Parameters
----------
cmd: list of str
the command to run (subprocess like).
subjects_dir: str, default None.
To set the $SUBJECTS_DIR environment variable.
add_fsl_env: bool, default False
To activate the FSL environment, required for commands like bbregister.
fsl_init: str
Path to the Bash script setting the FSL environment, if needed.
"""
fsprocess = FSWrapper(cmd)
if subjects_dir is not None:
fsprocess.environment["SUBJECTS_DIR"] = subjects_dir
if add_fsl_env:
fsl_env = environment(fsl_init)
for k, i in fsl_env.items():
if k not in fsprocess.environment:
fsprocess.environment[k] = i
else:
# A variable that exists in both FS and FSL environments
if k == "PATH":
fsprocess.environment["PATH"] += ":" + fsl_env["PATH"]
else:
pass # ignore this variable
fsprocess() # Run
if fsprocess.exitcode != 0:
raise FreeSurferRuntimeError(cmd[0], " ".join(cmd[1:]))
return fsprocess
def _environment(self) :
""" Return a dictionary of the environment needed by FSL binaries.
"""
# Check if FSL has already been configures
env = os.environ.get("FSL_CONFIGURED", None)
# Configure FSL
if env is None:
# Parse configuration file
env = environment(self.shfile)
# Save the result
os.environ["FSL_CONFIGURED"] = json.dumps(env)
# Load configuration
else:
env = json.loads(env)
return env
def _environment(self):
""" Return a dictionary of the environment needed by FSL binaries.
"""
# Check if FSL has already been configures
env = os.environ.get("FSL_CONFIGURED", None)
# Configure FSL
if env is None:
# Parse configuration file
env = environment(self.shfile)
# Save the result
os.environ["FSL_CONFIGURED"] = json.dumps(env)
# Load configuration
else:
env = json.loads(env)
return env
def register_diffusion_to_anatomy(outdir,
nodif_brain,
subject_id,
fs_subjects_dir = None,
subdir = "diff_to_anat",
fsl_init = "/etc/fsl/5.0/fsl.sh"):
"""
Register the diffusion to the anatomy (T1) using Freesurfer bbregister
(boundary-based registration).
<unit>
<input name="outdir" type="Directory" />
<input name="nodif_brain" type="File" />
<input name="subject_id" type="Str" />
<input name="fs_subjects_dir" type="Directory" />
<input name="subdir" type="Str" />
<input name="fsl_init" type="File" />
<output name="dif2anat_dat" type="File" description="
The .dat file created by tkregister/bbregister cmd." />
</unit>
"""
if fs_subjects_dir is None:
if "SUBJECTS_DIR" in os.environ:
fs_subjects_dir = os.environ["SUBJECTS_DIR"]
else:
raise ValueError("Missing <SUBJECTS_DIR>: set the $SUBJECTS_DIR "
"environment variable for Freesurfer or pass it "
"as an argument.")
# If a subdirectory name has been passed, adapt outdir
if subdir:
outdir = os.path.join(outdir, subdir)
# Create outdir if it does not exist
if not os.path.isdir(outdir):
os.makedirs(outdir)
dif2anat_dat = os.path.join(outdir, "dif2anat.dat")
cmd = ["bbregister", "--s", subject_id, "--mov", nodif_brain,
"--reg", dif2anat_dat, "--dti", "--init-fsl"]
fsprocess = FSWrapper(cmd)
fsprocess.environment["SUBJECTS_DIR"] = fs_subjects_dir
# bbregister requires FSL, so we have to add the FSL environment
fsl_env = environment(fsl_init)
for k, i in fsl_env.items():
if k not in fsprocess.environment:
fsprocess.environment[k] = i
else:
# A variable that exists in both FS and FSL environments
if k == "PATH":
fsprocess.environment["PATH"] += ":" + fsl_env["PATH"]
else:
pass # ignore this variable
fsprocess() # Run
if fsprocess.exitcode != 0:
raise FreeSurferRuntimeError(cmd[0], " ".join(cmd[1:]))
return dif2anat_dat