U f{j@s:dZddlZddlmZmZddZddZejdS)aDCreate 3-layer BEM model from Flash MRI images. Examples -------- .. code-block:: console $ mne flash_bem --subject=sample $ mne flash_bem -s sample -n --registered -5 sample/mri/mef05.mgz -3 sample/mri/mef30.mgz $ mne flash_bem -s sample -n --registered -5 sample/mri/flash/mef05_*.mgz -3 sample/mri/flash/mef30_*.mgz Notes ----- This program assumes that FreeSurfer and MNE are installed and sourced properly. This function extracts the BEM surfaces (outer skull, inner skull, and outer skin) from multiecho FLASH MRI data with spin angles of 5 and 30 degrees. The multiecho FLASH data can be input as .mgz or .nii files. This function assumes that the Freesurfer segmentation of the subject has been completed. In particular, the T1.mgz and brain.mgz MRI volumes should be, as usual, in the subject's mri directory. N)convert_flash_mrismake_flash_bemcCs|dks tg}|jD]N}|dddkr:t|dkr:qf|dddkrZt|dkrZqf||q|jdt|=t|j|j|dS)Nz---)AssertionErrorrargslenappendsetattrvaluesdest)optionopt_strvalueparserargrY/var/www/html/bwave/python/venv/lib/python3.8/site-packages/mne/commands/mne_flash_bem.py_vararg_callback s   rc Csddlm}|t}|jdddddd|jd d d d dd|jd ddddtdd|jddddtdd|jddddddd|jdd d!ddd"d|jd#d$d%ddd&d|jd'd(d)ddd*d|jd+d,d-dd.dd/|jd0d1d2dd3|jd4d5d6dd7d8|\}}|j}|j}|j}|dks4t |dkr8d9}|j }|dkrNd9}nt |dkr`d}|j }|j } |j } |j} |j} |j} |j}|jdkr|td:t|||||| d9d;}t||| | | || |d9d< dS)=z Run command.r) get_optparserz-sz --subjectsubjectz Subject nameN)r helpdefaultz-dz--subjects-dir subjects_dirzSubjects directoryz-3z --flash30z --noflash30flash30callbackzmThe 30-degree flip angle data. If no argument do not use flash30. If arguments are given, them as file names.)r actionrrz-5z--flash5flash5zFPath to the multiecho flash 5 images. Can be one file or one per echo.z-rz --registered registered store_trueFzNSet if the Flash MRI images have already been registered with the T1.mgz file.)r rrrz-nz --noconvert noconvertzV[DEPRECATED] Assume that the Flash MRI images have already been converted to mgz filesz-uz--unwarpunwarpzMRun grad_unwarp with -unwarp option on each of the converted data setsz-oz --overwrite overwritez-Write over existing .surf files in bem folderz-vz--viewshowz*Show BEM model in 3D for visual inspection)r rrrz--copycopyz+Use copies instead of symlinks for surfaces)r rrz-pz --flash-path flash_pathzs[DEPRECATED] The directory containing flash5.mgz files (defaults to $SUBJECTS_DIR/$SUBJECT/mri/flash/parameter_maps)r rrTz The subject argument must be set)rrrrconvertr"verbose) rrr#r$r&r%register flash5_imgr()Zmne.commands.utilsr__file__ add_optionr parse_argsrrrr rr!rr"r#r$r&r% print_help RuntimeErrorrr)rroptions_rrrrr'r)r"r#r$r&r%r*rrrrun0s              r2) __doc__ZmneZmne.bemrrrr2utilsZrun_command_if_mainrrrrs P