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Add auto-calculate for Brain Radius #3

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Add auto-calculate for Brain Radius #3

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23 changes: 22 additions & 1 deletion process_bold_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ def parse_args():
parser.add_argument('--fd_type', help='L1 (1) or L2 (2). Default: 1', type=int, default=1)
parser.add_argument('--fd_thr', help='Threshold level for framewise displacement (default: 0.2)', type=float, default=0.2)
parser.add_argument('--brain_radius', help='Estimate of brain radius in mm. Default: 50', type=int, default=50)
parser.add_argument('--auto_radius', help="Calculate head radius using brain mask and assuming it's a sphere", action='store_true')
parser.add_argument('--skip_sec', help='Seconds to skip at start of each functional run. Default: 0', type=float, default=0)
parser.add_argument('--lp_hz', help='Low-frequency cut-off for filtering signal. Default: 0.009', type=float, default=0.009)
parser.add_argument('--hp_hz', help='High-frequency cut-off for filtering signal. Default: 0.08', type=float, default=0.08)
Expand All @@ -48,6 +49,7 @@ def main(source_dir, subject, results_path, **kwargs):
fd_max = kwargs.get('fd_thr')
skip_seconds = kwargs.get('skip_sec')
brain_radius = kwargs.get('brain_radius')
auto_radius = True if 'auto_radius' in kwargs and kwargs['auto_radius'] else False
session_id = kwargs['session_id'] if 'session_id' in kwargs else False
lowpass_hz = kwargs.get('lp_hz')
highpass_hz = kwargs.get('hp_hz')
Expand Down Expand Up @@ -121,6 +123,8 @@ def main(source_dir, subject, results_path, **kwargs):
TR /= 1000 # account for ms in some headers
logger.info(f'TR: {TR} s')

if auto_radius:
brain_radius = calculate_brain_radius(SUBJECT_DIR, cii_input)
frisson_regressors = make_friston_regressors(settings['movement_regressors'].to_numpy(), brain_radius)
framewise_displacement, mean_framewise_displacement = calculate_framewise_displacement(
frisson_regressors[:, :6], FD_type=fd_type
Expand Down Expand Up @@ -438,7 +442,6 @@ def parcellate_data(data_path):
return ptseries_files

def create_functional_connectivity(parcellated_data_files, save_figs=False):

for data_file in parcellated_data_files:
ptseries_loaded = nb.load(data_file.resolve())
ptseries_data = ptseries_loaded.get_fdata()
Expand Down Expand Up @@ -466,6 +469,24 @@ def plot_framewise_displacement(output_dir, tr, framewise_displacement, cii_inpu
plt.savefig(save_fig_name.resolve(), format='png', dpi=300)
plt.close()

def calculate_brain_radius(source_dir, cii_input):
brain_mask_files = source_dir.glob(f'{cii_input.group(1)}_*_{cii_input.group(3)}_desc-brain_mask.nii.gz')
if len(brain_mask_files) >= 1:
brain_mask_file = brain_mask_files[0]
else:
raise RuntimeError(f'No brain mask found for {cii_input.group(1)} {cii_input.group(3)}')

brain_mask = nb.load(source_dir / f'{brain_mask_file}')
brain_mask_data = brain_mask.get_fdata()
voxel_volume = np.prod(brain_mask.header.get_zooms())
total_mask_voxels = np.sum(brain_mask_data)
total_mask_volume = voxel_volume * total_mask_voxels

brain_radius = ((3 * total_mask_volume) / (4 * np.pi)) ** (1 / 3)
logger.info(f'{cii_input.group(1)} {cii_input.group(3)} brain radius estimated to be {brain_radius} mm')
return brain_radius


def matrix_org3(figure_object, data_matrix, key, buffer, limits, color_map, colormap_data):
dim_y, dim_x = data_matrix.shape
if dim_y == dim_x:
Expand Down