Fix silent registration failure when paths contain spaces#40
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LalithShiyam wants to merge 1 commit intomasterfrom
Open
Fix silent registration failure when paths contain spaces#40LalithShiyam wants to merge 1 commit intomasterfrom
LalithShiyam wants to merge 1 commit intomasterfrom
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All subprocess calls to greedy and c3d used shell=True with unquoted f-string paths. When directory paths contained spaces (e.g., "psma vs acp3 patients"), the shell would split them into separate arguments causing greedy to fail silently — capture_output=True swallowed stderr and the return code was never checked. Replace re.escape() (regex escaping, wrong context) and bare f-string interpolation with shlex.quote() for proper shell escaping across all subprocess calls: rigid(), affine(), deformable(), _build_cmd(), and rgb2gray(). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
shell=Truewith unquoted f-string paths, causing silent failures when directory paths contained spacesre.escape()(regex escaping — wrong context) and bare path interpolation withshlex.quote()for proper shell escapingImageRegistration:rigid(),affine(),deformable(),_build_cmd()(resample), andrgb2gray()Problem
When a subject directory path contained spaces (e.g.,
psma vs acp3 patients/), the shell split the path into separate arguments. Greedy failed butcapture_output=Trueswallowed stderr and the return code was never checked — so PUMA logged alignment as "done" but no output files were created. This caused aFileNotFoundErrordownstream when trying to copy aligned masks.Test plan
psma vs acp3 patients/puma_input/)🤖 Generated with Claude Code