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Update script scil_viz_gradients_screenshot #1097

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merged 3 commits into from
Dec 18, 2024
Merged

Update script scil_viz_gradients_screenshot #1097

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c043822
Small update of read_bvals_bvecs
Dec 12, 2024
3d832a5
Fixing function bug
Dec 16, 2024
92fbb64
Points to bvecs
karanphil Dec 17, 2024
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12 changes: 5 additions & 7 deletions scripts/scil_viz_gradients_screenshot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
import os

from dipy.data import get_sphere
from dipy.io.gradients import read_bvals_bvecs

from scilpy.gradients.bvec_bval_tools import identify_shells
from scilpy.io.utils import (add_overwrite_arg,
Expand Down Expand Up @@ -88,7 +89,7 @@ def main():

if len(args.in_gradient_scheme) == 2:
assert_gradients_filenames_valid(parser, args.in_gradient_scheme,
'fsl')
True)
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Can you please put input_is_fsl=True, instead of only True?

elif len(args.in_gradient_scheme) == 1:
basename, ext = os.path.splitext(args.in_gradient_scheme[0])
if ext in ['.bvec', '.bvecs', '.bvals', '.bval']:
Expand All @@ -97,7 +98,7 @@ def main():
else:
assert_gradients_filenames_valid(parser,
args.in_gradient_scheme,
'mrtrix')
False)
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Same

else:
parser.error('Depending on the gradient format you should have '
'two files for FSL format and one file for MRtrix')
Expand All @@ -120,11 +121,8 @@ def main():
if len(args.in_gradient_scheme) == 2:
in_gradient_schemes = args.in_gradient_scheme
in_gradient_schemes.sort() # [bval, bvec]
# bvecs/bvals (FSL) format, X Y Z AND b (or transpose)
points = np.genfromtxt(in_gradient_schemes[1])
if points.shape[0] == 3:
points = points.T
bvals = np.genfromtxt(in_gradient_schemes[0])
bvals, points = read_bvals_bvecs(in_gradient_schemes[0],
in_gradient_schemes[1])
centroids, shell_idx = identify_shells(bvals)
else:
# MRtrix format X, Y, Z, b
Expand Down
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