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Consider uploading a T2starw spinal cord segmentation for sub-04 #56

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jcohenadad opened this issue Jan 16, 2024 · 1 comment · Fixed by #69
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Consider uploading a T2starw spinal cord segmentation for sub-04 #56

jcohenadad opened this issue Jan 16, 2024 · 1 comment · Fixed by #69
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jcohenadad commented Jan 16, 2024 •
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Instead of selecting another method only for sub-04:

rf-shimming-7t/data_processing.ipynb

Lines 200 to 202 in 5db1f0e

" # 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",

Consider uploading a manually corrected segmentation in the derivatives. This will be cleaner (and more scalable to other projects/data).

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@jcohenadad jcohenadad self-assigned this Jan 16, 2024
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Fixed in https://openneuro.org/datasets/ds004906/versions/2.4.0

@jcohenadad jcohenadad reopened this Jan 20, 2024
jcohenadad added a commit that referenced this issue Jan 20, 2024
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Using manual T2starw SC segmentation if it exists
c875ad6 
Fixes #56
@jcohenadad jcohenadad mentioned this issue Jan 20, 2024
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jcohenadad added a commit that referenced this issue Jan 20, 2024
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Use manual CSF mask and improve CSF/SC figure (#69)
bf4cf2f 
* Using manual T2starw SC segmentation if it exists

Fixes #56

* Get CSF masks from the derivatives

Fixes #67

* Fixed cropping and metric extraction for CSF

* Display CSF/SC instead of SC/CSF

Clearer to show the better on top

* Updated smoothing kernel to 40
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Use manual CSF mask and improve CSF/SC figure shimming-toolbox/rf-shimming-7t
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