From 595ec0863bcf0128edca6ed9add120594d7b368b Mon Sep 17 00:00:00 2001
From: jcohenadad <jcohen@polymtl.ca>
Date: Fri, 1 Nov 2024 17:32:04 -0400
Subject: [PATCH] Fixed: Cropping SNR *after* splitting

---
 data_processing-human.ipynb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/data_processing-human.ipynb b/data_processing-human.ipynb
index 90b9ba1..1cdae6b 100644
--- a/data_processing-human.ipynb
+++ b/data_processing-human.ipynb
@@ -229,11 +229,11 @@
     "\n",
     "for subject in subjects:\n",
     "    os.chdir(os.path.join(path_data, subject, \"fmap\"))\n",
+    "    # Split SNR data into sub-volumes (https://github.com/spinal-cord-7t/coil-qc-code/issues/34)\n",
+    "    !sct_image -i {subject}_acq-coilQaSagLarge_SNR.nii.gz -split t -o {subject}_acq-coilQaSagLarge_SNR.nii.gz\n",
     "    # Crop SNR data (https://github.com/spinal-cord-7t/coil-qc-code/issues/128)\n",
     "    !sct_crop_image -i {subject}_acq-coilQaSagLarge_SNR_T0000.nii.gz -xmax 450 -o {subject}_acq-coilQaSagLarge_SNR_T0000.nii.gz\n",
     "    !sct_crop_image -i {subject}_acq-coilQaSagLarge_SNR_T0000.nii.gz -m {subject}_acq-coilQaSagLarge_SNR_T0000.nii.gz -o {subject}_acq-coilQaSagLarge_SNR_T0000.nii.gz\n",
-    "    # Split SNR data into sub-volumes (https://github.com/spinal-cord-7t/coil-qc-code/issues/34)\n",
-    "    !sct_image -i {subject}_acq-coilQaSagLarge_SNR.nii.gz -split t -o {subject}_acq-coilQaSagLarge_SNR.nii.gz\n",
     "    # Segment spinal cord on SNR data, unless it already exists\n",
     "    fname_manual_seg = os.path.join(path_labels, subject, \"fmap\", f\"{subject}_acq-coilQaSagLarge_SNR_T0000_label-SC_seg.nii.gz\")\n",
     "    if os.path.exists(fname_manual_seg):\n",
@@ -313,7 +313,7 @@
     "for subject in subjects:\n",
     "# for subject in ['sub-MGH1']:\n",
     "    print(f\"\\n👉 CHECKING REGISTRATION FOR: {subject}\\n\")\n",
-    "    cmd = f\"fsleyes {subject}/fmap/{subject}_acq-coilQaSagLarge_SNR_T0000.nii.gz {subject}/fmap/{subject}_acq-coilQaSagLarge_SNR_T0000_seg_labeled.nii.gz --cmap rainbow\"\n",
+    "    cmd = f\"fsleyes {subject}/fmap/{subject}_acq-coilQaSagLarge_SNR_T0000.nii.gz {subject}/fmap/{subject}_acq-coilQaSagLarge_SNR_T0000_seg_labeled-UNIT1reg.nii.gz --cmap rainbow\"\n",
     "    print(cmd+\" &\")\n",
     "\n",
     "# TODO: undisplay all scans but the first"
@@ -1251,7 +1251,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "base",
+   "display_name": "myenv",
    "language": "python",
    "name": "python3"
   },