Use manual CSF mask and improve CSF/SC figure #69
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jcohenadad
commented
Jan 20, 2024
jcohenadad
commented
- Fixes Consider uploading a T2starw spinal cord segmentation for sub-04 #56
- Fixes Improve CSF mask #67
- Fixes Improve figure of SC/CSF ratio on T2starw #66
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Before/After changing the CSF masks:
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dpapp86
reviewed
Jan 21, 2024
| @@ -322,12 +336,12 @@ | |||
| "metadata": {}, | |||
| "outputs": [], | |||
| "source": [ | |||
| "# Make figure of SC/CSF signal ratio from T2starw scan\n", | |||
| "# Make figure of CSF/SC signal ratio from T2starw scan\n", | |||
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For me, this whole cell hangs for 10 minutes and then does not produce a figure
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Skipping it on a second pass and moving on
| " # Use another syntax for sub-04. See: https://github.com/shimming-toolbox/rf-shimming-7t/issues/31\n", | ||
| " if subject == 'sub-04':\n", | ||
| " !sct_deepseg_sc -i {subject}_acq-CoV_T2starw.nii.gz -c t2 -qc {path_qc}\n", | ||
| " fname_manual_seg = os.path.join(path_labels, subject, \"anat\", f\"{subject}_acq-CoV_T2starw_label-SC_seg.nii.gz\")\n", |
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Comment on the whole cell: the manual segmentation files are not found by the code, and do not seem to be present in the supplied labels, see #71
| @@ -400,7 +414,7 @@ | |||
| " ax.set_xticklabels([''] * len(original_vector))\n", | |||
| "\n", | |||
| " ax.set_title(f'{subject}', fontsize=font_size)\n", | |||
| " ax.set_ylabel('Cord/CSF T2starw signal ratio', fontsize=font_size)\n", | |||
| " ax.set_ylabel('CSF/Cord T2starw signal ratio', fontsize=font_size)\n", | |||
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Consider increasing the LineWidth to 3 or 5?
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@jcohenadad added review. Nothing really major |
This was referenced Jan 22, 2024
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