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fix val error when extracting recon size #353

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fix val error when extracting recon size #353

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e57533f
fix val error when extracting recon size
ramroomh Jun 20, 2025
89f7dd3
forces merge of dicoms
ramroomh Jun 27, 2025
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21 changes: 13 additions & 8 deletions pypet2bids/pypet2bids/dcm2niix4pet.py
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Original file line number Diff line number Diff line change
Expand Up @@ -480,7 +480,7 @@ def run_dcm2niix(self):
self.tempdir_location = tempdir_pathlike
# people use screwy paths, we do this before running dcm2niix to account for that
image_folder = helper_functions.sanitize_bad_path(self.image_folder)
cmd = f"{self.dcm2niix_path} -b y -w 1 -z y {file_format_args} -o {tempdir_pathlike} {image_folder}"
cmd = f"{self.dcm2niix_path} -b y -m Y -w 1 -z y -s y {file_format_args} -o {tempdir_pathlike} {image_folder}"
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@bendhouseart bendhouseart Jun 30, 2025

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Okay, sure I think this is fine as it passes on the phantoms and the other CI. I'm still not certain what it is that -s is doing:

-s : single file mode, do not convert other images in folder (y/n, default n)

But again, it's not affecting our CI so I'm pretty okay with it.

convert = subprocess.run(cmd, shell=True, capture_output=True)
self.telemetry_data["dcm2niix"] = {
"returncode": convert.returncode,
Expand Down Expand Up @@ -671,13 +671,18 @@ def run_dcm2niix(self):
else:
# collect filter size
recon_filter_size = ""
if re.search(
r"\d+.\d+", sidecar_json.get("ConvolutionKernel")
):
recon_filter_size = re.search(
r"\d+.\d*", sidecar_json.get("ConvolutionKernel")
)[0]
recon_filter_size = float(recon_filter_size)
if re.search(r"\d+.\d+", sidecar_json.get("ConvolutionKernel")):
try:
recon_filter_size = re.search(
r"\d+.\d*", sidecar_json.get("ConvolutionKernel")
)[0]
recon_filter_size = float(recon_filter_size)
except ValueError:
# If float conversion fails, try splitting and take first part
match_str = re.search(
r"\d+.\d*", sidecar_json.get("ConvolutionKernel")
)[0]
recon_filter_size = float(match_str.split()[0])
sidecar_json.update(
{"ReconFilterSize": float(recon_filter_size)}
)
Expand Down
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