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ds003416-mriqc/logs/duct/sub-cIIs02_2025.10.09T23.59.37-598988_stderr
Felix Hoffstaedter bfeb35ef56 [DATALAD RUNCMD] Compute MRIQC for sub-cIIs02 
=== Do not change lines below ===
{
 "chain": [],
 "cmd": "./code/containers/scripts/singularity_cmd exec code/containers/images/bids/bids-mriqc--24.0.2.sing mriqc sourcedata/raw . participant --participant-label sub-cIIs02 --no-datalad-get --no-sub --verbose --nprocs 1 --mem 3000 --work-dir /tmp --float32 --verbose-reports",
 "dsid": "aae8905a-985f-46fb-91f5-35c772654ddd",
 "exit": 0,
 "extra_inputs": [
  "code/containers/images/bids/bids-mriqc--24.0.2.sing"
 ],
 "inputs": [
  "sourcedata/raw/sub-cIIs02",
  "sourcedata/raw/dataset_description.json"
 ],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
2025-10-10 09:29:49 +02:00

218 lines
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/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: divide by zero encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: invalid value encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: divide by zero encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: invalid value encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: divide by zero encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: invalid value encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: divide by zero encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: invalid value encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: divide by zero encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: invalid value encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: divide by zero encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: invalid value encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: divide by zero encountered in divide
s = sum_m2 / (2 * K * sigma**2)
/opt/conda/lib/python3.11/site-packages/dipy/denoise/noise_estimate.py:252: RuntimeWarning: invalid value encountered in divide
s = sum_m2 / (2 * K * sigma**2)
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/opt/conda/lib/python3.11/site-packages/nireports/reportlets/mosaic.py:565: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`). Consider using `matplotlib.pyplot.close()`.
fig = plt.figure(layout=None)
/opt/conda/lib/python3.11/site-packages/nireports/reportlets/mosaic.py:565: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`). Consider using `matplotlib.pyplot.close()`.
fig = plt.figure(layout=None)
/opt/conda/lib/python3.11/site-packages/nireports/reportlets/modality/dwi.py:114: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`). Consider using `matplotlib.pyplot.close()`.
fig, axs = plt.subplots(
/opt/conda/lib/python3.11/site-packages/nireports/reportlets/modality/dwi.py:162: RuntimeWarning: divide by zero encountered in scalar divide
max_snr = imax / sigma
/opt/conda/lib/python3.11/site-packages/nireports/reportlets/modality/dwi.py:164: RuntimeWarning: invalid value encountered in divide
labels_bins_position = bins[0] * np.array(labels_bins) / max_snr
/opt/conda/lib/python3.11/site-packages/nireports/reportlets/modality/dwi.py:162: RuntimeWarning: divide by zero encountered in scalar divide
max_snr = imax / sigma
/opt/conda/lib/python3.11/site-packages/nireports/reportlets/modality/dwi.py:164: RuntimeWarning: invalid value encountered in divide
labels_bins_position = bins[0] * np.array(labels_bins) / max_snr
/opt/conda/lib/python3.11/site-packages/nireports/reportlets/modality/dwi.py:162: RuntimeWarning: divide by zero encountered in scalar divide
max_snr = imax / sigma
/opt/conda/lib/python3.11/site-packages/nireports/reportlets/modality/dwi.py:164: RuntimeWarning: invalid value encountered in divide
labels_bins_position = bins[0] * np.array(labels_bins) / max_snr
/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/anatomical.py:490: RuntimeWarning: divide by zero encountered in divide
bg_data[bg_data > 0] = bg_data[bg_data > 0] / bg_spread
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/displays/_slicers.py:420: UserWarning: empty mask
xmin_, xmax_, ymin_, ymax_, zmin_, zmax_ = get_mask_bounds(
/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/anatomical.py:490: RuntimeWarning: divide by zero encountered in divide
bg_data[bg_data > 0] = bg_data[bg_data > 0] / bg_spread
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/displays/_slicers.py:420: UserWarning: empty mask
xmin_, xmax_, ymin_, ymax_, zmin_, zmax_ = get_mask_bounds(
/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/anatomical.py:490: RuntimeWarning: divide by zero encountered in divide
bg_data[bg_data > 0] = bg_data[bg_data > 0] / bg_spread
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/displays/_slicers.py:420: UserWarning: empty mask
xmin_, xmax_, ymin_, ymax_, zmin_, zmax_ = get_mask_bounds(
/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/anatomical.py:490: RuntimeWarning: divide by zero encountered in divide
bg_data[bg_data > 0] = bg_data[bg_data > 0] / bg_spread
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/displays/_slicers.py:420: UserWarning: empty mask
xmin_, xmax_, ymin_, ymax_, zmin_, zmax_ = get_mask_bounds(
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/displays/_slicers.py:420: UserWarning: empty mask
xmin_, xmax_, ymin_, ymax_, zmin_, zmax_ = get_mask_bounds(
/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/anatomical.py:490: RuntimeWarning: divide by zero encountered in divide
bg_data[bg_data > 0] = bg_data[bg_data > 0] / bg_spread
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/displays/_slicers.py:420: UserWarning: empty mask
xmin_, xmax_, ymin_, ymax_, zmin_, zmax_ = get_mask_bounds(
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:234: RuntimeWarning: divide by zero encountered in scalar divide
cc_snr_estimates['shell0'] = round(float(in_b0[cc_mask].mean() / std_signal), decimals)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:257: RuntimeWarning: invalid value encountered in scalar divide
float(np.mean(mean_signal_worst / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:260: RuntimeWarning: invalid value encountered in scalar divide
float(np.mean(mean_signal_best / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:234: RuntimeWarning: divide by zero encountered in scalar divide
cc_snr_estimates['shell0'] = round(float(in_b0[cc_mask].mean() / std_signal), decimals)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:257: RuntimeWarning: divide by zero encountered in scalar divide
float(np.mean(mean_signal_worst / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:260: RuntimeWarning: divide by zero encountered in scalar divide
float(np.mean(mean_signal_best / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:234: RuntimeWarning: divide by zero encountered in scalar divide
cc_snr_estimates['shell0'] = round(float(in_b0[cc_mask].mean() / std_signal), decimals)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:257: RuntimeWarning: invalid value encountered in scalar divide
float(np.mean(mean_signal_worst / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:260: RuntimeWarning: invalid value encountered in scalar divide
float(np.mean(mean_signal_best / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:234: RuntimeWarning: divide by zero encountered in scalar divide
cc_snr_estimates['shell0'] = round(float(in_b0[cc_mask].mean() / std_signal), decimals)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:257: RuntimeWarning: divide by zero encountered in scalar divide
float(np.mean(mean_signal_worst / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:260: RuntimeWarning: divide by zero encountered in scalar divide
float(np.mean(mean_signal_best / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:234: RuntimeWarning: divide by zero encountered in scalar divide
cc_snr_estimates['shell0'] = round(float(in_b0[cc_mask].mean() / std_signal), decimals)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:257: RuntimeWarning: invalid value encountered in scalar divide
float(np.mean(mean_signal_worst / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:260: RuntimeWarning: invalid value encountered in scalar divide
float(np.mean(mean_signal_best / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:234: RuntimeWarning: divide by zero encountered in scalar divide
cc_snr_estimates['shell0'] = round(float(in_b0[cc_mask].mean() / std_signal), decimals)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:257: RuntimeWarning: invalid value encountered in scalar divide
float(np.mean(mean_signal_worst / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:260: RuntimeWarning: invalid value encountered in scalar divide
float(np.mean(mean_signal_best / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:234: RuntimeWarning: divide by zero encountered in scalar divide
cc_snr_estimates['shell0'] = round(float(in_b0[cc_mask].mean() / std_signal), decimals)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:257: RuntimeWarning: divide by zero encountered in scalar divide
float(np.mean(mean_signal_worst / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:260: RuntimeWarning: divide by zero encountered in scalar divide
float(np.mean(mean_signal_best / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:234: RuntimeWarning: divide by zero encountered in scalar divide
cc_snr_estimates['shell0'] = round(float(in_b0[cc_mask].mean() / std_signal), decimals)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:257: RuntimeWarning: invalid value encountered in scalar divide
float(np.mean(mean_signal_worst / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:260: RuntimeWarning: invalid value encountered in scalar divide
float(np.mean(mean_signal_best / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:234: RuntimeWarning: divide by zero encountered in scalar divide
cc_snr_estimates['shell0'] = round(float(in_b0[cc_mask].mean() / std_signal), decimals)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:257: RuntimeWarning: divide by zero encountered in scalar divide
float(np.mean(mean_signal_worst / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:260: RuntimeWarning: divide by zero encountered in scalar divide
float(np.mean(mean_signal_best / std_signal)), decimals
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/img_plotting.py:557: RuntimeWarning: overflow encountered in scalar subtract
ptp = 0.5 * (vmax - vmin)
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/nireports/interfaces/reporting/base.py:105: UserWarning: The given float value must not exceed 0. But, you have given threshold=0.001.
mask_nii = threshold_img(fixed_image_nii, 1e-3)
/opt/conda/lib/python3.11/site-packages/mriqc/qc/diffusion.py:220: ExtremeValueWarning: CC mask is too small (0 voxels)
warn(f'CC mask is too small ({nvox_cc} voxels)', ExtremeValueWarning, stacklevel=1)
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