diff --git a/dwiqc/__version__.py b/dwiqc/__version__.py index 7d768ee..d881953 100644 --- a/dwiqc/__version__.py +++ b/dwiqc/__version__.py @@ -1,6 +1,6 @@ __title__ = 'dwiqc' __description__ = 'Quality Assurance Pipeline for Diffusion MR Data' __url__ = 'https://github.com/harvard-nrg/dwiqc' -__version__ = '1.3.16' +__version__ = '1.3.17' __author__ = 'Neuroinformatics Research Group' __author_email__ = 'info@neuroinfo.org' diff --git a/dwiqc/tasks/qsiprep.py b/dwiqc/tasks/qsiprep.py index 47f5698..204f090 100644 --- a/dwiqc/tasks/qsiprep.py +++ b/dwiqc/tasks/qsiprep.py @@ -351,18 +351,6 @@ def extract_vols(self, dwi_full_path, dwi_basename): def run_extract(self, dwi_full_path, bval_path, epi_out_path): - #module('load','fsl/6.0.4-ncf') - - #print(self._fsl_sif) - - #extract_command = f"singularity exec {self._fsl_sif} /APPS/fsl/bin/select_dwi_vols {dwi_full_path} {bval_path} {epi_out_path} 0" - - #extract_command = f'select_dwi_vols {dwi_full_path} {bval_path} {epi_out_path} 0' - - #proc1 = subprocess.check_output(extract_command, shell=True, stderr=subprocess.STDOUT, text=True) - - #logger.info(proc1) - bvec_path = bval_path.replace('.bval', '.bvec') bvals, bvecs = read_bvals_bvecs(bval_path, bvec_path) @@ -382,7 +370,6 @@ def run_extract(self, dwi_full_path, bval_path, epi_out_path): b0_string = ','.join(b0_volumes) - #extract_command = f"singularity exec {self._fsl_sif} /APPS/fsl/bin/fslselectvols -i {dwi_full_path} -o {epi_out_path} --vols={b0_string}" os.makedirs(self._outdir, exist_ok=True) @@ -395,8 +382,6 @@ def run_extract(self, dwi_full_path, bval_path, epi_out_path): except subprocess.CalledProcessError as e: print(e.stdout) - #logger.info(proc1) - def insert_json_value(self, key, value, json_file): """