Select the FOV and target resolution of the phantom

from snake.core import Phantom, SimConfig, GreConfig
from snake.core.engine.utils import get_ideal_phantom
from snake.toolkit.plotting import axis3dcut

shape = (90, 110,90) Original FOV And size of the phantom

shape = (181, 217, 181)
fov_mm = (181, 217, 181)
TR = 50
TE = 30
FA = 40  # np.degrees(np.arccos(np.exp((-TR/2000))))
field = "7T"  # "1T5"

sim_conf = SimConfig(
    max_sim_time=3, seq=GreConfig(TR=TR, TE=TE, FA=FA), fov_mm=fov_mm, shape=shape
)
sim_conf.hardware.n_coils = 32  # Update to get multi coil results.
sim_conf.hardware.field_strength = 7

sim_conf.res_mm

(1.0, 1.0, 1.0)

phantom = Phantom.from_brainweb(sub_id=4, sim_conf=sim_conf, tissue_file="tissue_1T5")

Traceback (most recent call last):
  File "/home/runner/work/snake-fmri/snake-fmri/examples/anatomical/example_fov_select.py", line 30, in <module>
    phantom = Phantom.from_brainweb(sub_id=4, sim_conf=sim_conf, tissue_file="tissue_1T5")
  File "/home/runner/work/snake-fmri/snake-fmri/src/snake/core/phantom/static.py", line 112, in from_brainweb
    tissues_mask = get_mri(sub_id, contrast="fuzzy").astype(np.float32)
  File "/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/brainweb_dl/mri.py", line 173, in get_mri
    data = _get_mri_sub20(
  File "/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/brainweb_dl/mri.py", line 91, in _get_mri_sub20
    filename = get_brainweb20(
  File "/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/brainweb_dl/_brainweb.py", line 329, in get_brainweb20
    Parallel(n_jobs=-1, backend="threading")(
  File "/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/joblib/parallel.py", line 2007, in __call__
    return output if self.return_generator else list(output)
  File "/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/joblib/parallel.py", line 1650, in _get_outputs
    yield from self._retrieve()
  File "/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/joblib/parallel.py", line 1754, in _retrieve
    self._raise_error_fast()
  File "/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/joblib/parallel.py", line 1789, in _raise_error_fast
    error_job.get_result(self.timeout)
  File "/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/joblib/parallel.py", line 745, in get_result
    return self._return_or_raise()
  File "/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/joblib/parallel.py", line 763, in _return_or_raise
    raise self._result
requests.exceptions.ConnectTimeout: HTTPConnectionPool(host='brainweb.bic.mni.mcgill.ca', port=80): Max retries exceeded with url: /cgi/brainweb1/?do_download_alias=subject04_bck&format_value=raw_short&zip_value=gnuzip&download_for_real=%5BStart+download%21%5D (Caused by ConnectTimeoutError(<urllib3.connection.HTTPConnection object at 0x7f2a322094e0>, 'Connection to brainweb.bic.mni.mcgill.ca timed out. (connect timeout=None)'))

sim_conf

from snake.core.handlers.fov import FOVHandler


# the center and size target_res are all in millimeters.
fov_handler = FOVHandler(
    center=(90, 110, 100),
    size=(192, 192, 128),
    angles=(5, 0, 0),
    target_res=(2.0, 2.0, 2.0),
)

new_phantom = fov_handler.get_static(phantom, sim_conf)

new_contrast = get_ideal_phantom(new_phantom, sim_conf)

new_contrast.shape

axis3dcut(new_contrast.T, z_score=None, cuts=(0.5, 0.6, 0.5))