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Use only the lowest shell in calculation of the CSD response function. #1089

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merged 3 commits into from
Jan 26, 2024
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Use only the lowest shell in calculation of the CSD response function. #1089

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bce5ae9
Use only the lowest shell in calculation of the CSD response function.
arokem Jan 16, 2024
d91928e
Use only the part of the data corresponding to the lowest shell.
arokem Jan 17, 2024
1cb52ed
Only restrict to that portion if you need to.
arokem Jan 17, 2024
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14 changes: 13 additions & 1 deletion AFQ/models/csd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,10 @@
from dipy.reconst import csdeconv as csd
from dipy.reconst import mcsd
from dipy.reconst import shm
from dipy.core.gradients import gradient_table, unique_bvals_magnitude
import AFQ.utils.models as ut


# Monkey patch fixed spherical harmonics for conda from
# DIPY dev:
from AFQ._fixes import spherical_harmonics
Expand Down Expand Up @@ -37,7 +39,17 @@ def _model(gtab, data, response=None, sh_order=None):

my_model = csd.ConstrainedSphericalDeconvModel
if response is None:
response, _ = csd.auto_response_ssst(gtab, data, roi_radii=10,
unique_bvals = unique_bvals_magnitude(gtab.bvals)
if len(unique_bvals[unique_bvals > 0]) > 1:
low_shell_idx = gtab.bvals <= unique_bvals[unique_bvals > 0][0]
response_gtab = gradient_table(gtab.bvals[low_shell_idx],
gtab.bvecs[low_shell_idx])
data = data[..., low_shell_idx]
else:
response_gtab = gtab
response, _ = csd.auto_response_ssst(response_gtab,
data,
roi_radii=10,
fa_thr=0.7)
# Catch conditions where an auto-response could not be calculated:
if np.all(np.isnan(response[0])):
Expand Down
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