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@drcandacemakedamoore
drcandacemakedamoore committed Sep 6, 2024
1 parent aa876e3 commit 7c677d4
Showing 1 changed file with 255 additions and 46 deletions.
301 changes: 255 additions & 46 deletions notebooks/hand_examiner.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,8 @@
"file1 = os.path.join(file_path, \"001.nii.gz\")\n",
"file2 = os.path.join(file_path, \"002.nii.gz\")\n",
"file3 = os.path.join(file_path, \"003.nii.gz\")\n",
"file4 = os.path.join(file_path, \"004.nii.gz\")"
"file4 = os.path.join(file_path, \"004.nii.gz\")\n",
"file5 = os.path.join(file_path, \"005.nii.gz\")"
]
},
{
Expand All @@ -98,6 +99,7 @@
},
"outputs": [],
"source": [
"level = 12\n",
"loaded1 = nib.load(file1)\n",
"loaded_object1 = loaded1.dataobj\n",
"loaded2 = nib.load(file2)\n",
Expand All @@ -106,28 +108,45 @@
"loaded_object3 = loaded3.dataobj\n",
"loaded4 = nib.load(file4)\n",
"loaded_object4 = loaded4.dataobj\n",
"loaded5 = nib.load(file5)\n",
"loaded_object5 = loaded5.dataobj\n",
"plt.figure(figsize=(16,16))\n",
"f, ax =plt.subplots(4,4)\n",
"ax[0,0].imshow(loaded_object1[:,:,6,0], cmap='grey')\n",
"ax[0,1].imshow(loaded_object1[:,:,6,1], cmap='grey')\n",
"ax[0,2].imshow(loaded_object1[:,:,6,2], cmap='grey')\n",
"ax[0,3].imshow(loaded_object1[:,:,6,3], cmap='grey')\n",
"ax[0,0].imshow(loaded_object1[:,:,level,0], cmap='grey')\n",
"ax[0,1].imshow(loaded_object1[:,:,level,1], cmap='grey')\n",
"ax[0,2].imshow(loaded_object1[:,:,level,2], cmap='grey')\n",
"ax[0,3].imshow(loaded_object1[:,:,level,3], cmap='grey')\n",
"ax[0,0].set_title('001')\n",
"ax[1,0].imshow(loaded_object2[:,:,6,0], cmap='grey')\n",
"ax[1,1].imshow(loaded_object2[:,:,6,1], cmap='grey')\n",
"ax[1,2].imshow(loaded_object2[:,:,6,2], cmap='grey')\n",
"ax[1,3].imshow(loaded_object2[:,:,6,3], cmap='grey')\n",
"ax[1,0].imshow(loaded_object2[:,:,level,0], cmap='grey')\n",
"ax[1,1].imshow(loaded_object2[:,:,level,1], cmap='grey')\n",
"ax[1,2].imshow(loaded_object2[:,:,level,2], cmap='grey')\n",
"ax[1,3].imshow(loaded_object2[:,:,level,3], cmap='grey')\n",
"ax[1,0].set_title('002')\n",
"ax[2,0].imshow(loaded_object3[:,:,6,0], cmap='grey')\n",
"ax[2,1].imshow(loaded_object3[:,:,6,1], cmap='grey')\n",
"ax[2,2].imshow(loaded_object3[:,:,6,2], cmap='grey')\n",
"ax[2,3].imshow(loaded_object3[:,:,6,3], cmap='grey')\n",
"ax[2,0].imshow(loaded_object3[:,:,level,0], cmap='grey')\n",
"ax[2,1].imshow(loaded_object3[:,:,level,1], cmap='grey')\n",
"ax[2,2].imshow(loaded_object3[:,:,level,2], cmap='grey')\n",
"ax[2,3].imshow(loaded_object3[:,:,level,3], cmap='grey')\n",
"ax[2,0].set_title('003')\n",
"ax[3,0].imshow(loaded_object4[:,:,6,0], cmap='grey')\n",
"ax[3,1].imshow(loaded_object4[:,:,6,1], cmap='grey')\n",
"ax[3,2].imshow(loaded_object4[:,:,6,2], cmap='grey')\n",
"ax[3,3].imshow(loaded_object4[:,:,6,3], cmap='grey')\n",
"ax[3,0].set_title('004')"
"ax[3,0].imshow(loaded_object4[:,:,level,0], cmap='grey')\n",
"ax[3,1].imshow(loaded_object4[:,:,level,1], cmap='grey')\n",
"ax[3,2].imshow(loaded_object4[:,:,level,2], cmap='grey')\n",
"ax[3,3].imshow(loaded_object4[:,:,level,3], cmap='grey')\n",
"ax[3,0].set_title('004')\n",
"# ax[3,0].imshow(loaded_object5[:,:,level,0], cmap='grey')\n",
"# ax[3,1].imshow(loaded_object5[:,:,level,1], cmap='grey')\n",
"# ax[3,2].imshow(loaded_object5[:,:,level,2], cmap='grey')\n",
"# ax[3,3].imshow(loaded_object5[:,:,level,3], cmap='grey')\n",
"# ax[3,0].set_title('005')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "1037c308-e9e8-42a2-a7f6-eb5877f2bcbe",
"metadata": {},
"outputs": [],
"source": [
"print(loaded_object5.shape)"
]
},
{
Expand All @@ -139,14 +158,101 @@
},
"outputs": [],
"source": [
"loaded2 = nib.load(file2)\n",
"loaded_object2 = loaded2.dataobj\n",
"# And here is Brick 5 which has all the variants\n",
"plt.figure()\n",
"f, ax =plt.subplots(1,4)\n",
"ax[0].imshow(loaded_object2[:,:,0,0], cmap='grey')\n",
"ax[1].imshow(loaded_object2[:,:,0,1], cmap='grey')\n",
"ax[2].imshow(loaded_object2[:,:,0,2], cmap='grey')\n",
"ax[3].imshow(loaded_object2[:,:,0,3], cmap='grey')"
"ax[0].imshow(loaded_object5[:,:,9,0], cmap='grey')\n",
"ax[1].imshow(loaded_object5[:,:,9,1], cmap='grey')\n",
"ax[2].imshow(loaded_object5[:,:,9,2], cmap='grey')\n",
"ax[3].imshow(loaded_object5[:,:,9,3], cmap='grey')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "c1699549-b787-4537-9109-b46699e93ffe",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"# maybe the last one is actually an M0?\n",
"plt.imshow(loaded_object5[:,:,14,3], cmap='grey')"
]
},
{
"cell_type": "markdown",
"id": "8cca8eae-ed7e-4e12-992f-6e2ec6ea376e",
"metadata": {},
"source": [
"We suspect that what we should have run is the following, with the rightmost image as the M0"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "faa425d4-545b-4b9d-9d93-25feeae66ce1",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"extra2 = '/mnt/data/raw_data/5extra1/NOT_DIAGNOSTIC_Raw_eASL_3_delays/600_NOT_DIAGNOSTIC_Raw_eASL_3_delays_20221214000000_real.nii.gz'\n",
"extra2= nib.load(extra2)\n",
"loaded5 = extra2.dataobj\n",
"print(loaded5.shape)\n",
"plt.figure()\n",
"f, ax =plt.subplots(1,5)\n",
"ax[0].imshow(loaded5[:,:,14,0], cmap='grey')\n",
"ax[1].imshow(loaded5[:,:,14,1], cmap='grey')\n",
"ax[2].imshow(loaded5[:,:,14,2], cmap='grey')\n",
"ax[3].imshow(loaded5[:,:,14,3], cmap='grey')\n",
"ax[4].imshow(loaded5[:,:,14,4], cmap='grey')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "c2676d36-af15-4338-a169-01c40eeaf455",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"# A look at the M0 more closely\n",
"plt.imshow(loaded5[:,:,14,4], cmap='grey')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ce8f00fd-eecb-454b-a5c2-e41078a65b31",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"# here we will load an extra image\n",
"#/mnt/data/output/transfer_2217763_files_3b695c8d/BRICK-005/BRICK-005/20221214/MR/\n",
"#NOT_DIAGNOSTIC_(CBF)_eASL_3_delays/601_NOT_DIAGNOSTIC_(CBF)_eASL_3_delays_NOT_DIAGNOSTIC_(CBF)_eASL_3_delays_20221214000000_real.nii.gz \n",
"extra1_for5 = nib.load('/mnt/data/raw_data/5extra1/NOT_DIAGNOSTIC_CBF_eASL_3_delays/601_NOT_DIAGNOSTIC_CBF_eASL_3_delays_real.nii.gz')\n",
"\n",
"loaded5 = extra1_for5.dataobj\n",
"print(loaded5.shape)\n",
"plt.imshow(loaded5[:,:,11], cmap='grey')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5d760009-659d-401d-bc45-9f0d40ffca3f",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"## we also had a set of \"\"CASL images\" we did no analyse\n",
"#nib.load('Z:/output/transfer_2217763_files_3b695c8d/BRICK-004/BRICK-004/20220704/MR/eASL_3_delays/005_eASL_3_delays_eASL_3_delays_20220704000000_real.nii.gz')"
]
},
{
Expand All @@ -157,8 +263,109 @@
"tags": []
},
"outputs": [],
"source": [
"## some files have a raw and other dataset\n",
"## such as brick 5, let's examine that"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "afff45ab-0573-4c2f-bbf3-66d987a4ed2b",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"five_base = '/mnt/data/output/transfer_2217763_files_3b695c8d/BRICK-005/BRICK-005/20221214/MR/'\n",
"\n",
"brick5extra1 = os.path.join(\n",
" five_base, \n",
" 'NOT_DIAGNOSTIC_\\(CBF\\)_eASL_3_delays/',\n",
" '601_NOT_DIAGNOSTIC_\\(CBF\\)_eASL_3_delays_NOT_DIAGNOSTIC_\\(CBF\\)_eASL_3_delays_20221214000000_real.nii.gz'\n",
" \n",
")\n",
" \n",
"print(brick5extra1) \n"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "350537cf-5537-4b39-a4fd-985f2e20d6f2",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "c270b82b-cc1b-4013-a2c0-79145147021a",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"extra1 = nib.load('/mnt/data/raw_data/5extra1/NOT_DIAGNOSTIC_CBF_eASL_3_delays/601_NOT_DIAGNOSTIC_CBF_eASL_3_delays_real.nii.gz')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b7eae791-8bc2-4556-a93e-9041de204e2a",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "fc8e8fcd-4034-4e20-b2db-ebe89f37d6fa",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "ead56335-4a3d-4fb2-a9a7-279d3c57b12b",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "0e00273d-7eea-43fc-af5a-ed4af126a4a2",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "10aedaba-3f6c-4b68-8f7d-33a9292f28fa",
"metadata": {},
"outputs": [],
"source": [
"/mnt/data/output/transfer_2217763_files_3b695c8d/BRICK-005/BRICK-005/20221214/MR/NOT_DIAGNOSTIC_\\(CBF\\)_eASL_3_delays/601_NOT_DIAGNOSTIC_\\(CBF\\)_eASL_3_delays_NOT_DIAGNOSTIC_\\(CBF\\)_eASL_3_delays_20221214000000_real.\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "c858f847-ddda-4e7f-b0c3-b3f34087c380",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"brick5extra1 = nib.load(\n",
" os.path.join(\n",
" base_path,\"BRICK-005/BRICK-005/20221214/MR/\",\"\\'NOT_DIAGNOSTIC_(CBF)_eASL_3_delays\\'\")\n",
")"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand All @@ -180,8 +387,8 @@
},
"outputs": [],
"source": [
"# base_path = \"/mnt/data/MRIs/transfer_2217763_files_3b695c8d\"\n",
"# folders = glob.glob(os.path.join(base_path, '**', 'MR'), recursive=True)\n",
"base_path = \"/mnt/data/MRIs/transfer_2217763_files_3b695c8d\"\n",
"folders = glob.glob(os.path.join(base_path, '**', 'MR'), recursive=True)\n",
"# #print(folders)"
]
},
Expand All @@ -206,24 +413,24 @@
},
"outputs": [],
"source": [
"folder_names = []\n",
"eASLs = []\n",
"NOT_DIAGNOSTIC_CBF_eASL_3_delays = []\n",
"for folder in folders:\n",
" if os.path.isdir(os.path.join(folder, 'eASL_3_delays')):\n",
" folder_names.append((folder[46:]))\n",
" eASLs.append('exists')\n",
" else:\n",
" folder_names.append(folder)\n",
" eASLs.append('NO exists')\n",
"# folder_names = []\n",
"# eASLs = []\n",
"# NOT_DIAGNOSTIC_CBF_eASL_3_delays = []\n",
"# for folder in folders:\n",
"# if os.path.isdir(os.path.join(folder, 'eASL_3_delays')):\n",
"# folder_names.append((folder[46:]))\n",
"# eASLs.append('exists')\n",
"# else:\n",
"# folder_names.append(folder)\n",
"# eASLs.append('NO exists')\n",
" \n",
" if os.path.isdir(os.path.join(folder, 'NOT_DIAGNOSTIC_(CBF)_eASL_3_delays')): \n",
" NOT_DIAGNOSTIC_CBF_eASL_3_delays.append('exists')\n",
" else:\n",
" NOT_DIAGNOSTIC_CBF_eASL_3_delays.append('NOT exists')\n",
"data = {'folder':folder_names, 'basic_ASL':eASLs,'NOT_DIAGNOSTIC_CBF_eASL_3_delays': NOT_DIAGNOSTIC_CBF_eASL_3_delays}\n",
"frame =pd.DataFrame(data)\n",
"frame"
"# if os.path.isdir(os.path.join(folder, 'NOT_DIAGNOSTIC_(CBF)_eASL_3_delays')): \n",
"# NOT_DIAGNOSTIC_CBF_eASL_3_delays.append('exists')\n",
"# else:\n",
"# NOT_DIAGNOSTIC_CBF_eASL_3_delays.append('NOT exists')\n",
"# data = {'folder':folder_names, 'basic_ASL':eASLs,'NOT_DIAGNOSTIC_CBF_eASL_3_delays': NOT_DIAGNOSTIC_CBF_eASL_3_delays}\n",
"# frame =pd.DataFrame(data)\n",
"# frame"
]
},
{
Expand All @@ -235,7 +442,7 @@
},
"outputs": [],
"source": [
"import re\n",
"#import re\n",
"\n",
"def brick_id(col):\n",
" return re.sub(r'.*/BRICK-(\\d\\d\\d)/.*', r'\\1', col['asls'])\n",
Expand Down Expand Up @@ -274,7 +481,7 @@
"metadata": {},
"outputs": [],
"source": [
"Brick 1, 2, 3, 4, 7 -21, 23, 24, 25*, 27,28,31,32,33,35, "
"# Brick 1, 2, 3, 4, 7 -21, 23, 24, 25*, 27,28,31,32,33,35, "
]
},
{
Expand All @@ -283,7 +490,9 @@
"id": "c314dfc7-0390-4c75-a783-4d4f4141e19b",
"metadata": {},
"outputs": [],
"source": []
"source": [
"asls"
]
},
{
"cell_type": "code",
Expand Down

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