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[BUG]: Fix FSL std2imgcoord I/O #278

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Dec 5, 2023
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[BUG]: Fix FSL std2imgcoord I/O #278

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e67c9bc
fix: use piped input for FSL std2imgcoord
synchon Dec 5, 2023
c4218d7
chore: add changelog 278.bugfix
synchon Dec 5, 2023
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1 change: 1 addition & 0 deletions docs/changes/newsfragments/278.bugfix
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
Bypass FSL ``std2imgcoord`` stdin bug and use recommended piped input for coordinates transformation by `Synchon Mandal`_
7 changes: 4 additions & 3 deletions junifer/data/coordinates.py
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Expand Up @@ -260,11 +260,12 @@ def get_coordinates(
std2imgcoord_out_path = element_tempdir / "coordinates_transformed.txt"
# Set std2imgcoord command
std2imgcoord_cmd = [
"std2imgcoord",
"cat",
f"{pretransform_coordinates_path.resolve()}",
"| std2imgcoord",
f"-img {target_data['reference_path'].resolve()}",
f"-warp {extra_input['Warp']['path'].resolve()}",
f"{pretransform_coordinates_path.resolve()}",
f"> {std2imgcoord_out_path.resolve()}",
f"- > {std2imgcoord_out_path.resolve()}",
]
# Call std2imgcoord
std2imgcoord_cmd_str = " ".join(std2imgcoord_cmd)
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