Introduced path_qc variable

Analysis.ipynb

@@ -73,13 +73,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Download data\n",
+    "# Download data and define path variables\n",
     "\n",
     "!datalad install https://github.com/OpenNeuroDatasets/ds004906.git\n",
     "os.chdir(\"ds004906\")\n",
     "# !datalad get . # uncomment for production\n",
     "!datalad get sub-01/  # comment for debugging\n",
-    "path_data = os.getcwd()"
+    "path_data = os.getcwd()\n",
+    "path_qc = os.path.join(path_data, \"qc\")"
    ]
   },
   {
@@ -94,21 +95,21 @@
     "subjects = glob.glob(\"sub-*\")\n",
     "for subject in subjects:\n",
     "    os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
-    "    !sct_deepseg_sc -i {subject}_acq-CoV_T2starw.nii.gz -c t2 -qc {os.path.join(path_data, \"qc\")}"
+    "    !sct_deepseg_sc -i {subject}_acq-CoV_T2starw.nii.gz -c t2 -qc {path_qc}"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "028b3383",
+   "id": "17223063",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Register TFL B1maps to the GRE scan\n",
     "\n",
     "for subject in subjects:\n",
     "    os.chdir(os.path.join(path_data, subject, \"fmap\"))\n",
-    "    !sct_register_multimodal -i {subject}_acq-anatCoV_TB1TFL.nii.gz -d ../anat/{subject}_acq-CoV_T2starw.nii.gz -param step=1,type=im,algo=slicereg,metric=CC -qc {os.path.join(path_data, \"qc\")}"
+    "    !sct_register_multimodal -i {subject}_acq-anatCoV_TB1TFL.nii.gz -d ../anat/{subject}_acq-CoV_T2starw.nii.gz -param step=1,type=im,algo=slicereg,metric=CC -qc {path_qc}"
    ]
   }
  ],