Add MPRAGE processing and visualisation #46
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@jcohenadad please review This should contain everything needed to process MPRAGE scans and create the associated figure |
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also adresses #38 |
dpapp86
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jcohenadad
reviewed
Jan 13, 2024
data_processing.ipynb
Outdated
| @@ -163,13 +168,14 @@ | |||
| "source": [ | |||
| "# Define useful variables\n", | |||
| "\n", | |||
| "path_data = os.getcwd()\n", | |||
| "path_data = os.getcwd() #works if and only if this is run first and once. Otherwise it will pick up whatever the current directory is if someone wanted to rerun it\n", | |||
jcohenadad
reviewed
Jan 13, 2024
data_processing.ipynb
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| "# shim_modes = [\"CP\", \"CoV\"] # debugging\n", | ||
| "print(f\"shim_modes: {shim_modes}\")\n", | ||
| "subjects = sorted(glob.glob(\"sub-*\"))\n", | ||
| "subjects = sorted(glob.glob(\"sub-*\")) #Same problem with rerunning it if the cwd is not the ds004906 root\n", |
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jcohenadad
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Jan 13, 2024
jcohenadad
reviewed
Jan 13, 2024
jcohenadad
reviewed
Jan 13, 2024
jcohenadad
reviewed
Jan 13, 2024
jcohenadad
reviewed
Jan 13, 2024
data_processing.ipynb
Outdated
| @@ -259,12 +269,12 @@ | |||
| "metadata": {}, | |||
| "outputs": [], | |||
| "source": [ | |||
| "# Extract the signal intensity on the GRE scan within the spinal cord between levels C1 and T2 (included)\n", | |||
| "# Extract the signal intensity on the GRE scan within the spinal cord between levels C3 and T2 (included)\n", | |||
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This change is outside the scope of this PR.
that should go in the PR body-- i've added it |
jcohenadad
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Jan 16, 2024
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on 36bb2d7 I'm getting:
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
Cell In[9], line 8
6 os.chdir(os.path.join(path_data, subject, "anat"))
7 CoV_flatten=glob.glob(os.path.join(path_data, subject, "anat", f"{subject}_acq-CoV_T1w_crop_flatten.nii.gz"))
----> 8 CoV_flatten=CoV_flatten[0]
9 CoV_flatten_data=nib.load(CoV_flatten).get_fdata()
10 CP_flatten=glob.glob(os.path.join(path_data, subject, "anat", f"{subject}_acq-CP_T1w_reg_flatten.nii.gz"))
IndexError: list index out of rangeFalse alarm: I forgot to run required cells before :🤦
jcohenadad
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Jan 16, 2024
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Jan 16, 2024
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Clarifies text wrt choice of CoV GRE and MPRAGE for segmentation
Fixes #37
Fixes #38
Fixes #39
Fixes #43
Fixes #45