Only run generate figure for one subject

Author: jcohenadad

data_processing-human.ipynb

@@ -958,31 +958,30 @@
     "# Co-register subjects across sites for better visualisation\n",
     "\n",
     "sites = [\"CRMBM\", \"UCL\", \"MNI\", \"MGH\", \"MPI\", \"NTNU\", \"MSSM\"]\n",
-    "subject_ids = ['3']  # [\"1\",\"2\",\"3\"] JCA: Given that we create a figure showing only subject 3 I think we can skip the others for the sake of time\n",
+    "subject_id = '3'  # Subject number to generate figures from\n",
     "site_ref = 'CRMBM'\n",
     "vert_labels = '3'  # vertebral levels for alignment between sites\n",
     "\n",
     "files_anat = [\"acq-anat_TB1TFL\", \"acq-famp_TB1DREAM\",\"acq-coilQaSagLarge_SNR_T0000\"]  # image that serves as a reference to get the segmentation\n",
     "files_metric = [\"TFLTB1map\", \"DREAMTB1avgB1map\",\"acq-coilQaSagLarge_SNR_T0000\"]  # coilQA image to display on the figure\n",
     "\n",
-    "for subject_id in subject_ids:\n",
-    "    for site in sites:\n",
-    "        print(f\"👉 PROCESSING: {site}{subject_id}\")\n",
-    "        for file_anat, file_metric in zip(files_anat, files_metric):\n",
-    "            os.chdir(os.path.join(path_data, \"sub-\"+site+subject_id, \"fmap\"))\n",
-    "            # Extract vertebral labels\n",
-    "            !sct_label_utils -i sub-{site}{subject_id}_{file_name}_seg_labeled-UNIT1reg.nii.gz -vert-body {vert_labels} -o sub-{site}{subject_id}_{file_name}_labels.nii.gz\n",
-    "            # Co-register data to reference subject\n",
-    "            if site != \"CRMBM\":\n",
-    "                !sct_register_multimodal \\\n",
-    "                    -i sub-{site}{subject_id}_{file_metric}.nii.gz \\\n",
-    "                    -iseg sub-{site}{subject_id}_{file_anat}_seg.nii.gz \\\n",
-    "                    -ilabel sub-{site}{subject_id}_{file_anat}_labels.nii.gz \\\n",
-    "                    -d ../../sub-{site_ref}{subject_id}/fmap/sub-{site_ref}{subject_id}_{file_metric}.nii.gz \\\n",
-    "                    -dseg ../../sub-{site_ref}{subject_id}/fmap/sub-{site_ref}{subject_id}_{file_anat}_seg.nii.gz \\\n",
-    "                    -dlabel ../../sub-{site_ref}{subject_id}/fmap/sub-{site_ref}{subject_id}_{file_anat}_labels.nii.gz \\\n",
-    "                    -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=seg,iter=0 \\\n",
-    "                    -x nn"
+    "for site in sites:\n",
+    "    print(f\"👉 PROCESSING: {site}{subject_id}\")\n",
+    "    for file_anat, file_metric in zip(files_anat, files_metric):\n",
+    "        os.chdir(os.path.join(path_data, \"sub-\"+site+subject_id, \"fmap\"))\n",
+    "        # Extract vertebral labels\n",
+    "        !sct_label_utils -i sub-{site}{subject_id}_{file_anat}_seg_labeled-UNIT1reg.nii.gz -vert-body {vert_labels} -o sub-{site}{subject_id}_{file_anat}_labels.nii.gz\n",
+    "        # Co-register data to reference subject\n",
+    "        if site != \"CRMBM\":\n",
+    "            !sct_register_multimodal \\\n",
+    "                -i sub-{site}{subject_id}_{file_metric}.nii.gz \\\n",
+    "                -iseg sub-{site}{subject_id}_{file_anat}_seg.nii.gz \\\n",
+    "                -ilabel sub-{site}{subject_id}_{file_anat}_labels.nii.gz \\\n",
+    "                -d ../../sub-{site_ref}{subject_id}/fmap/sub-{site_ref}{subject_id}_{file_metric}.nii.gz \\\n",
+    "                -dseg ../../sub-{site_ref}{subject_id}/fmap/sub-{site_ref}{subject_id}_{file_anat}_seg.nii.gz \\\n",
+    "                -dlabel ../../sub-{site_ref}{subject_id}/fmap/sub-{site_ref}{subject_id}_{file_anat}_labels.nii.gz \\\n",
+    "                -param step=0,type=label,dof=Tx_Ty_Tz:step=1,type=seg,iter=0 \\\n",
+    "                -x nn"
    ]
   },
   {
@@ -1071,14 +1070,14 @@
     "    axes=axes.flatten() \n",
     "    for i,site in enumerate(sites):\n",
     "        # Load data\n",
-    "        os.chdir(os.path.join(path_data, f\"sub-{site}{ind_subject}\", \"fmap\"))\n",
+    "        os.chdir(os.path.join(path_data, f\"sub-{site}{subject_id}\", \"fmap\"))\n",
     "        if site == site_ref:\n",
     "            suffix = \"\"\n",
     "        else:\n",
     "            suffix = \"_reg\"\n",
-    "        map = nib.load(f\"sub-{site}{ind_subject}_{file_metric}{suffix}_flatten.nii.gz\")\n",
+    "        map = nib.load(f\"sub-{site}{subject_id}_{file_metric}{suffix}_flatten.nii.gz\")\n",
     "        # map = nib.load(f\"sub-{site}{ind_subject}_{file_metric}{suffix}.nii.gz\")\n",
-    "        slices = slicing_indices[file_metric][ind_subject]\n",
+    "        slices = slicing_indices[file_metric][subject_id]\n",
     "        data = map.get_fdata()[slices[0], slices[1], round(map.get_fdata().shape[2] / 2)]\n",
     "\n",
     "        # Figure configuration\n",
@@ -1129,7 +1128,7 @@
     "legend_types = [\"1/g\", \"[arb]\"]\n",
     "\n",
     "# Select individual subject to show\n",
-    "ind_subject = '2'\n",
+    "ind_subject = '2'  # Here we select subject 2 because it has the most complete data\n",
     "\n",
     "mean_gfac = {}\n",
     "max_gfac = {}\n",
@@ -1223,7 +1222,7 @@
     "sites = [\"CRMBM\", \"UCL\", \"MNI\", \"MGH\", \"MPI\", \"NTNU\", \"MSSM\"]\n",
     "\n",
     "# Select subject to show\n",
-    "subject = '1'\n",
+    "subject = '1'  # and here we select subject 1 because it has the most complete data\n",
     "\n",
     "        \n",
     "for i,site in enumerate(sites):\n",