Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Use manual CSF mask and improve CSF/SC figure #69

Merged
merged 5 commits into from
Jan 20, 2024
Merged

Use manual CSF mask and improve CSF/SC figure #69

Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
c875ad6
Using manual T2starw SC segmentation if it exists
jcohenadad Jan 20, 2024
45aae5d
Get CSF masks from the derivatives
jcohenadad Jan 20, 2024
87660ed
Fixed cropping and metric extraction for CSF
jcohenadad Jan 20, 2024
099728c
Display CSF/SC instead of SC/CSF
jcohenadad Jan 20, 2024
06407df
Updated smoothing kernel to 40
jcohenadad Jan 20, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
72 changes: 43 additions & 29 deletions data_processing.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -205,13 +205,44 @@
"\n",
"for subject in subjects:\n",
" os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
" # 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",
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

" if os.path.exists(fname_manual_seg):\n",
" # Manual segmentation already exists. Copy it to local folder\n",
" print(f\"{subject}: Manual segmentation found\\n\")\n",
" shutil.copyfile(fname_manual_seg, f\"{subject}_acq-CoV_T2starw_seg.nii.gz\")\n",
" # Generate QC report to make sure the manual segmentation is correct\n",
" !sct_qc -i {subject}_acq-CoV_T2starw.nii.gz -s {subject}_acq-CoV_T2starw_seg.nii.gz -p sct_deepseg_sc -qc {path_qc} -qc-subject {subject}\n",
" else:\n",
" # Manual segmentation does not exist. Run automatic segmentation.\n",
" print(f\"{subject}: Manual segmentation not found\")\n",
" !sct_deepseg_sc -i {subject}_acq-CoV_T2starw.nii.gz -c t2s -qc {path_qc}"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "eb9a9267",
"metadata": {},
"outputs": [],
"source": [
"# Copy CSF masks from the derivatives folder\n",
"\n",
"# For more details about how these masks were created, see: https://github.com/shimming-toolbox/rf-shimming-7t/issues/67\n",
"\n",
"for subject in subjects:\n",
" os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
" fname_manual_seg = os.path.join(path_labels, subject, \"anat\", f\"{subject}_acq-CoV_T2starw_label-CSF_seg.nii.gz\")\n",
" if os.path.exists(fname_manual_seg):\n",
" # Manual segmentation already exists. Copy it to local folder\n",
" print(f\"{subject}: Manual segmentation found\\n\")\n",
" shutil.copyfile(fname_manual_seg, f\"{subject}_acq-CoV_T2starw_label-CSF_seg.nii.gz\")\n",
" # Generate QC report to make sure the manual segmentation is correct\n",
" !sct_qc -i {subject}_acq-CoV_T2starw.nii.gz -s {subject}_acq-CoV_T2starw_label-CSF_seg.nii.gz -p sct_deepseg_sc -qc {path_qc} -qc-subject {subject}\n",
" else:\n",
" # Manual segmentation does not exist. Panic!\n",
" print(f\"{subject}: Manual segmentation not found 😱\")"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand All @@ -224,7 +255,8 @@
"for subject in subjects:\n",
" os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
" !sct_crop_image -i {subject}_acq-CoV_T2starw.nii.gz -m {subject}_acq-CoV_T2starw_seg.nii.gz -dilate 20x20x0 -o {subject}_acq-CoV_T2starw_crop.nii.gz\n",
" !sct_crop_image -i {subject}_acq-CoV_T2starw_seg.nii.gz -m {subject}_acq-CoV_T2starw_seg.nii.gz -dilate 20x20x0 -o {subject}_acq-CoV_T2starw_crop_seg.nii.gz"
" !sct_crop_image -i {subject}_acq-CoV_T2starw_seg.nii.gz -m {subject}_acq-CoV_T2starw_seg.nii.gz -dilate 20x20x0 -o {subject}_acq-CoV_T2starw_crop_seg.nii.gz\n",
" !sct_crop_image -i {subject}_acq-CoV_T2starw_label-CSF_seg.nii.gz -m {subject}_acq-CoV_T2starw_seg.nii.gz -dilate 20x20x0 -o {subject}_acq-CoV_T2starw_crop_label-CSF_seg.nii.gz"
]
},
{
Expand Down Expand Up @@ -254,7 +286,6 @@
"source": [
"# Register *_T2starw to CoV_T2starw\n",
jcohenadad marked this conversation as resolved.
Show resolved Hide resolved
"\n",
"# Commenting for now, due to https://github.com/shimming-toolbox/rf-shimming-7t/issues/35\n",
"for subject in subjects:\n",
" os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
" for shim_mode in shim_modes:\n",
Expand All @@ -263,23 +294,6 @@
" !sct_register_multimodal -i {subject}_acq-{shim_mode}_T2starw.nii.gz -d {subject}_acq-CoV_T2starw_crop.nii.gz -dseg {subject}_acq-CoV_T2starw_crop_seg.nii.gz -param step=1,type=im,algo=dl -qc {path_qc}"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "eb9a9267",
"metadata": {},
"outputs": [],
"source": [
"# Create CSF mask by dilating the spinal cord segmentation\n",
"\n",
"for subject in subjects:\n",
" os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
" !sct_maths -i {subject}_acq-CoV_T2starw_crop_seg.nii.gz -dilate 3 -shape disk -dim 2 -o {subject}_acq-CoV_T2starw_crop_seg_dilate.nii.gz\n",
" !sct_maths -i {subject}_acq-CoV_T2starw_crop_seg_dilate.nii.gz -sub {subject}_acq-CoV_T2starw_crop_seg.nii.gz -o {subject}_acq-CoV_T2starw_crop_CSFseg.nii.gz\n",
" # Generate QC report to assess CSF mask\n",
" !sct_qc -i {subject}_acq-CoV_T2starw_crop.nii.gz -s {subject}_acq-CoV_T2starw_crop_CSFseg.nii.gz -p sct_deepseg_sc -qc {path_qc} -qc-subject {subject}"
]
},
{
"cell_type": "markdown",
"id": "aac9d889",
Expand All @@ -303,7 +317,7 @@
"\n",
"for subject in subjects:\n",
" os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
" for shim_method in ['CoV', 'CP']: # TODO: shim_modes:\n",
" for shim_method in shim_modes:\n",
" # Shim methods are registered to the CoV T2starw scan, so we need to use the added suffix to identify them\n",
" if shim_method == 'CoV':\n",
" file_suffix = 'crop'\n",
Expand All @@ -312,7 +326,7 @@
" fname_result_sc = os.path.join(path_results, f\"{subject}_acq-{shim_method}_T2starw_label-SC.csv\")\n",
" !sct_extract_metric -i {subject}_acq-{shim_method}_T2starw_{file_suffix}.nii.gz -f {subject}_acq-CoV_T2starw_crop_seg.nii.gz -method wa -vert 3:9 -vertfile {subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz -perslice 1 -o {fname_result_sc}\n",
" fname_result_csf = os.path.join(path_results, f\"{subject}_acq-{shim_method}_T2starw_label-CSF.csv\")\n",
" !sct_extract_metric -i {subject}_acq-{shim_method}_T2starw_{file_suffix}.nii.gz -f {subject}_acq-CoV_T2starw_crop_CSFseg.nii.gz -method wa -vert 3:9 -vertfile {subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz -perslice 1 -o {fname_result_csf}"
" !sct_extract_metric -i {subject}_acq-{shim_method}_T2starw_{file_suffix}.nii.gz -f {subject}_acq-CoV_T2starw_crop_label-CSF_seg.nii.gz -method wa -vert 3:9 -vertfile {subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz -perslice 1 -o {fname_result_csf}"
jcohenadad marked this conversation as resolved.
Show resolved Hide resolved
]
},
{
Expand All @@ -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",
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

For me, this whole cell hangs for 10 minutes and then does not produce a figure

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Skipping it on a second pass and moving on

"\n",
"# Go back to root data folder\n",
"os.chdir(path_data)\n",
"\n",
"def smooth_data(data, window_size=20):\n",
"def smooth_data(data, window_size=40):\n",
jcohenadad marked this conversation as resolved.
Show resolved Hide resolved
" \"\"\" Apply a simple moving average to smooth the data. \"\"\"\n",
" return uniform_filter1d(data, size=window_size, mode='nearest')\n",
"\n",
Expand Down Expand Up @@ -360,7 +374,7 @@
"for i, subject in enumerate(subjects):\n",
" ax = axes[i]\n",
"\n",
" for shim_method in ['CoV', 'CP']: # TODO: shim_modes:\n",
" for shim_method in shim_modes:\n",
" # Initialize list to collect data for this shim method\n",
" method_data = []\n",
"\n",
Expand All @@ -375,7 +389,7 @@
" data_csf = df['WA()']\n",
" \n",
" # Compute ratio\n",
" data_sc_csf_ratio = data_sc / data_csf\n",
" data_sc_csf_ratio = data_csf / data_sc\n",
jcohenadad marked this conversation as resolved.
Show resolved Hide resolved
"\n",
" # Normalize the x-axis to a 0-1 scale for each subject\n",
" x_subject = np.linspace(0, 1, len(data_sc_csf_ratio))\n",
Expand All @@ -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",
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Consider increasing the LineWidth to 3 or 5?

" ax.tick_params(axis='y', which='major', labelsize=font_size-4)\n",
"\n",
" # Add legend only to the first subplot\n",
Expand Down