def dist_corr_basket(img: MincAtom,
dc_img: MincAtom):
stage = CmdStage(inputs=(img,), outputs=(dc_img,), memory=4,
cmd=['distortion_correction_september_2014.pl',
'-spawn','-output-dir', img.pipeline_sub_dir,
img.path])
print(stage.render())
stage.set_log_file(log_file_name=os.path.join(img.pipeline_sub_dir,"dist_corr.log"))
return Result(stages=Stages([stage]), output=dc_img)
def crop_to_brain(img: MincAtom,
cropped_img: MincAtom,
crop_to_brain_options):
stage = CmdStage(inputs=(img,), outputs=(cropped_img,), memory=4,
cmd=['crop_to_brain.py',
'--bbox_x',str(crop_to_brain_options.bbox_x),
'--bbox_y',str(crop_to_brain_options.bbox_y),
'--bbox_z',str(crop_to_brain_options.bbox_z),
'--intermediate_bbox=1.5',
'--buffer_z',str(crop_to_brain_options.buffer_z),
'--clobber',
img.path, cropped_img.path])
print(stage.render())
stage.set_log_file(log_file_name=os.path.join(img.pipeline_sub_dir,"crop_to_brain.log"))
return Result(stages=Stages([stage]), output=cropped_img)
def varian_recon_ge3dmice_saddle(fids: List[FileAtom],
imgs: List[MincAtom],
varian_recon_options,
output_dir: str):
stage = CmdStage(inputs=tuple(fids), outputs=tuple(imgs), memory=25,
cmd=['mri_recon.py', 'ge3dmice_sg_cylA' , '--petable_ordered_pairs', '--grappa_coil_decouple',
'--outputreps', '--phasedriftcorr',
'--mouse_list',varian_recon_options.mouse_list,
'--petable',varian_recon_options.petable,
'--grappa_coil_groupings',varian_recon_options.grappa_coil_groupings,
'--procpar_file_name', varian_recon_options.procpar_file_name,
'--clobber', '--fermi_ellipse' if varian_recon_options.fermi_ellipse else '',
varian_recon_options.fid_input_directory,
os.path.join(output_dir,varian_recon_options.output_file_name)])
print(stage.render())
stage.set_log_file(log_file_name=os.path.join(output_dir,"varian_recon.log"))
return Result(stages=Stages([stage]), output=imgs)
