def mt_link_inputs( input_dir, link_to_dir, change_to_dir = True ): cenc_dirs = cenc.directories( input_dir ) util.mkcd_dir( [ link_to_dir ], change_to_dir ) input_files = cenc_dirs['mt']['inputs'] label_files = cenc_dirs['mt']['labels'] util.link_inputs( input_files + label_files, link_to_dir )
def prepare( cenc_participant_dir ): freesurfer_input_dir = os.path.join( cenc_participant_dir, 'freesurfer', 'input' ) util.mkcd_dir( [ freesurfer_input_dir ]) input_files = [ os.path.join( cenc_participant_dir, 'reorient', 't1w.nii.gz'), os.path.join( cenc_participant_dir, 'reorient', 't2flair.nii.gz'), os.path.join( cenc_participant_dir, 'reorient', 't2tse.nii.gz') ] util.link_inputs( input_files, freesurfer_input_dir) return
def prepare( input_dir ): cenc_dirs = cenc.directories( input_dir ) util.mkcd_dir( [ cenc_dirs['freesurfer']['input'] ]) input_files = [ os.path.join( cenc_dirs['cenc']['reorient'], 't1w.nii.gz'), os.path.join( cenc_dirs['cenc']['reorient'], 't2flair.nii.gz'), os.path.join( cenc_dirs['cenc']['reorient'], 't2tse.nii.gz') ] util.link_inputs( input_files, cenc_dirs['freesurfer']['input'] ) return
def methods_01_register(input_dir, verbose): cenc_dirs = cenc.directories(input_dir) wm_lesions_dir = cenc_dirs['wmlesions']['dirs']['root'] wm_lesions_lpa_dir = cenc_dirs['wmlesions']['dirs']['lpa'] # Register util.mkcd_dir([cenc_dirs['wmlesions']['dirs']['register']], True) files = [ os.path.join(cenc_dirs['wmlesions']['dirs']['input'], 'nu.nii.gz'), os.path.join(cenc_dirs['wmlesions']['dirs']['input'], 't2flair.nii.gz'), os.path.join(cenc_dirs['results']['dirs']['labels'], 'mask.nii.gz') ] util.link_inputs(files, cenc_dirs['wmlesions']['dirs']['register']) ants_register('t2flair')
def prepare(input_dir): cenc_dirs = cenc.directories(input_dir) wm_lesions_dir = cenc_dirs['wmlesions']['dirs']['root'] wm_lesions_input_dir = cenc_dirs['wmlesions']['dirs']['input'] wm_lesions_lpa_dir = cenc_dirs['wmlesions']['dirs']['lpa'] # Create Input Directory if it doesn't exist and link files files = [ os.path.abspath( os.path.join(cenc_dirs['results']['dirs']['images'], 'nu.nii.gz')), os.path.abspath( os.path.join(cenc_dirs['results']['dirs']['labels'], 'mask.nii.gz')), os.path.abspath( os.path.join(cenc_dirs['cenc']['reorient'], 't2flair.nii.gz')) ] util.mkcd_dir(os.path.join(wm_lesions_input_dir)) util.link_inputs(files, wm_lesions_input_dir)
participant_dir = os.path.abspath(os.path.join(inArgs.cenc_dir, id)) reorient_dir = util.path_relative_to(participant_dir, inArgs.reorient_dir) wm_lesions_dir = util.path_relative_to(participant_dir, inArgs.out_dir) wm_lesions_input_dir = os.path.join(wm_lesions_dir, 'input') wm_lesions_lpa_dir = os.path.join(wm_lesions_dir, '01-lst_lpa') wm_lesions_lga_dir = os.path.join(wm_lesions_dir, '02-lst_lga') # Create Output Directory if it doesn't exist files = [ os.path.abspath(os.path.join(reorient_dir, 't1w.nii.gz')), os.path.abspath(os.path.join(reorient_dir, 't2flair.nii.gz')) ] util.mkcd_dir(os.path.join(wm_lesions_input_dir)) util.link_inputs(files, wm_lesions_input_dir) # util.mkcd_dir(os.path.join(wm_lesions_lpa_dir), False) util.mkcd_dir(os.path.join(wm_lesions_lga_dir), True) util.copy_inputs(files, wm_lesions_lga_dir) for ii in glob.glob('*.gz'): os.system('gunzip ' + ii) util.link_inputs(glob.glob('*.nii'), wm_lesions_lpa_dir)
else: tarball_filename = id + '_fmri.tar.gz' if os.path.isfile(os.path.join(out_dir, tarball_filename)): sys.exit('fMRI tarball already exists for ' + id + '.') # Create Output Directory if it doesn't exist files = [ os.path.abspath(os.path.join(dicom_dir, 'dcmConvertAll.cfg')), os.path.abspath(os.path.join(dicom_dir, 'dcmConvert_cenc.cfg')), os.path.abspath(os.path.join(nifti_dir, 'rest.nii.gz')) ] util.mkcd_dir(out_dir) util.link_inputs(files, out_dir) files_to_be_tarred = glob.glob('*') # Create TarBall tarball = tarfile.open(tarball_filename, 'w:gz') for f in files_to_be_tarred: tarball.add(f) tarball.close() # Clean Directory for ii in files_to_be_tarred:
affine_out_wras_to_wlps = stage1_output_files[1] affine_out_wlps_to_wctf = stage1_output_files[3] fiducials_out_iras = stage1_output_files[2] fiducials_out_wlps = stage1_output_files[4] fiducials_out_wctf = stage1_output_files[5] print stage1_output_files if inArgs.run and (1 in inArgs.run_stage): util.print_stage("Entering Stage 1 - Creating matrices", inArgs.verbose) util.verify_inputs(stage1_input_files, inArgs.verbose) util.mkcd_dir( stage1_directory ) util.link_inputs( stage1_input_files, stage1_directory) # # Save ITK affine matrix # if inArgs.verbose: print print "Image affine RAS image to RAS world matrix" print img_affine_matrix_ras print util.save_itk_affine_matrix( img_affine_matrix_ras, affine_out_iras_to_wras, inArgs.verbose )
out_fiducials_ctf = util.path_relative_to( stage1_directory, inArgs.out_ctf ) out_fiducials_native = util.path_relative_to( stage1_directory, inArgs.out_native ) out_fiducials_template = util.path_relative_to( stage1_directory, inArgs.out_template ) stage1_input_files = stage0_output_files stage1_output_files = [ affine_iras_to_wlps, affine_iras_to_wlps, affine_wlps_to_wctf, out_fiducials_ctf, out_fiducials_native, out_fiducials_template ] if inArgs.run and (1 in inArgs.run_stage): util.print_stage('Entering Stage 1 - Calculating affine matrices', inArgs.verbose) util.verify_inputs(stage1_input_files, inArgs.verbose) util.mkcd_dir( stage1_directory ) util.link_inputs( stage1_input_files, stage1_directory) # iCSA to wLPS util.extract_affine( image_native, affine_iras_to_wlps, True, False, inArgs.verbose) ctf.icsa_to_wlps( fiducials_native_icsa, inArgs.out_native, affine_iras_to_wlps, inArgs.verbose, inArgs.debug ) # wLPS to wCTF # When transforming points use the inverse. I have no idea why. Ask ANTs. ctf.calc_matrix( inArgs.out_native, affine_wlps_to_wctf, 1.0, inArgs.verbose) ctf.wlps_to_wctf( inArgs.out_native, inArgs.out_ctf, affine_wlps_to_wctf, inArgs.verbose, inArgs.debug) # wLPS to wTemplate native_to_template_transform = [ template_to_native[1], template_to_native[0] ]