ENH: Improve FLASH BEM support

[larsoner]

I thought it would be trivial to get MBP to run FLASH for ds000117, but it wasn't. I ended up needing to read some MRI JSON files and write some files:

FLASH synthesis code

"""Create FLASH BEM surfaces for ds000117.

https://openneuro.org/datasets/ds000117/versions/1.0.5

Reconstructed with FreeSurfer::

    $ export SUBJECT=sub-09 && export SUBJECTS_DIR=~/mne_data/ds000117-full/derivatives/subjects && mkdir -p ${SUBJECTS_DIR}/${SUBJECT}/mri/orig && mri_convert ~/mne_data/ds000117-full/${SUBJECT}/ses-mri/anat/${SUBJECT}_ses-mri_acq-mprage_T1w.nii.gz ${SUBJECTS_DIR}/${SUBJECT}/mri/orig/001.mgz && recon-all -all -subjid ${SUBJECT}
"""

import json
import pathlib
import subprocess

import mne

data_path = pathlib.Path('~/mne_data/ds000117-full').expanduser().resolve(True)
subjects_dir = data_path / 'derivatives' / 'subjects'
subjects_dir.mkdir(exist_ok=True)
echos = [
    json.loads((data_path / f'run-1_echo-{ei}_FLASH.json').read_text())
    for ei in range(1, 8)
]

for subj_num in range(1, 17):
    print('*' * 80)
    subject = f'sub-{subj_num:02d}'
    print(f'Running subject {subject}')
    print('*' * 80)
    in_dir = data_path / subject / 'ses-mri' / 'anat'
    out_dir = subjects_dir / subject / 'mri' / 'flash'
    out_dir.mkdir(exist_ok=True)
    for ei, echo in enumerate(echos, 1):
        in_flash = in_dir / f'{subject}_ses-mri_run-1_echo-{ei}_FLASH.nii.gz'
        out_flash = out_dir / f'mef05_{ei:03d}.mgz'
        if out_flash.is_file():
            continue
        tr = echo['RepetitionTime'] * 1000
        te = echo['EchoTime'] * 1000
        cmd = [
            'mri_convert',
            '-tr', f'{tr}',
            '-te', f'{te}',
            '-flip_angle', '5',
            str(in_flash),
            str(out_flash),
        ]
        subprocess.check_call(cmd)
    pm_fname = out_dir / 'parameter_maps' / 'flash5.mgz'
    if not pm_fname.is_file():
        mne.bem.convert_flash_mris(
            subject=subject, subjects_dir=subjects_dir,
            flash5=True, flash30=False)
    assert pm_fname.is_file()
    bem_dir = subjects_dir / subject / 'bem'
    if not (bem_dir / 'inner_skull.surf').is_file():
        mne.bem.make_flash_bem(
            subject=subject, subjects_dir=subjects_dir, overwrite=True,
            show=True, register=True, verbose=True)

I think in principle if the FLASH info exists, we should be able to do the individual-echo writing and synthesis if necessary. Perhaps we are cheating a bit with ds000248 because subjects/sub-01/mri/flash/mef05.mgz already exists.

Or maybe instead we should propose amending ds000117 with the mef05.mgz already present...

[agramfort]

it's very possible we hard coded stuff for ds00248

have you tried the pipeline with ds000117? that can be a good test bed

Message ID: @.***>

[larsoner]

We discussed this in the latest dev meeting -- we could try to add support for this via a get_flash_image callable, but it's tricky for ds000117 because its FreeSurfer derivatives are incomplete (T1.mgz isn't even there) and organized in a non-standard way (nested as derivatives/freesurfer/sub-01/ses-mri/anat/surf etc. rather than derivatives/freesurfer/sub-01/surf).

My suggestion would be to add this if we see that there are others who would benefit from it...