Adding config file for training the 2D segmentation model

README.md

@@ -14,13 +14,13 @@ git clone https://github.com/ivadomed/model_seg_csf_epi.git
 
 ## Get the data
 
-- [email protected]:datasets/data_gre-epi
+- [email protected]:datasets/mni-bmpd
 
 ### Example calls to get the data
 
 ~~~
-git clone [email protected]:datasets/data_gre-epi
-cd data_gre-epi
+git clone [email protected]:datasets/mni-bmpd
+cd mni-bmpd
 git annex get .
 cd ..
 ~~~

config/seg_csf_2D.json → config/mni_bmpd_csf-2d.json

@@ -1,16 +1,24 @@
 {
     "command": "train",
     "gpu_ids": [2],
-    "path_output": "/mnt/duke/temp/rohan/data_training_human_sc_csf_moco/initial_run",
+    "path_output": "/mnt/duke/temp/rohan/data_training_human_sc_csf/initial_run",
     "model_name": "test_model",
     "debugging": true,
     "object_detection_params": {
         "object_detection_path": null,
         "safety_factor": [1.0, 1.0, 1.0]
     },
+
+    "wandb": {
+        "wandb_api_key": "<api key>",
+        "project_name": "data_training_human_sc_csf",
+        "run_name": "run-2d"
+
+    },
+
 
     "loader_parameters": {
-        "path_data": "/mnt/duke/temp/rohan/data_training_human_sc_csf_moco/BIDS_conv",
+        "path_data": "/mnt/duke/temp/rohan/data_training_human_sc_csf/processed_data",
         "subject_selection": {"n": [], "metadata": [], "value": []},
         "target_suffix": ["_seg-manual"],
         "extensions": [".nii.gz"],
@@ -49,7 +57,7 @@
             "name": "DiceLoss"
         },
         "training_time": {
-            "num_epochs": 1,
+            "num_epochs": 20,
             "early_stopping_patience": 50,
             "early_stopping_epsilon": 0.001
         },

preprocessing/preprocess.sh

@@ -0,0 +1,85 @@
+#!/bin/bash
+#
+# Process data. 
+#     For T1 : From raw images, proceeds to resampling and reorientation to RPI.
+#     
+#     Crop all images.
+#     Generates soft segmentations.
+# Usage:
+#   ./process_data.sh <SUBJECT>
+#
+#
+# Authors: Rohan Banerjee
+
+# The following global variables are retrieved from the caller sct_run_batch
+# but could be overwritten by uncommenting the lines below:
+# PATH_DATA_PROCESSED="~/data_processed"
+# PATH_RESULTS="~/results"
+# PATH_LOG="~/log"
+# PATH_QC="~/qc"
+
+# Uncomment for full verbose
+set -x
+
+# Exit if user presses CTRL+C (Linux) or CMD+C (OSX)
+trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
+
+# Print retrieved variables from sct_run_batch to the log (to allow easier debug)
+echo “Retrieved variables from from the caller sct_run_batch:”
+echo “PATH_DATA: ${PATH_DATA}”
+echo “PATH_DATA_PROCESSED: ${PATH_DATA_PROCESSED}”
+echo “PATH_RESULTS: ${PATH_RESULTS}”
+echo “PATH_LOG: ${PATH_LOG}”
+echo “PATH_QC: ${PATH_QC}”
+
+# Retrieve input params
+SUBJECT=$1
+
+# echo SUBJECT
+
+# Save script path
+PATH_SCRIPT=$PWD
+
+get starting time:
+start=`date +%s`
+
+# SCRIPT STARTS HERE
+# ==============================================================================
+# Display useful info for the log, such as SCT version, RAM and CPU cores available
+sct_check_dependencies -short
+
+# Go to folder where data will be copied and processed
+cd $PATH_DATA_PROCESSED
+
+
+Copy list of participants in processed data folder
+if [[ ! -f "participants.tsv" ]]; then
+  rsync -avzh $PATH_DATA/participants.tsv .
+fi
+
+if [[ ! -f "participants.json" ]]; then
+  rsync -avzh $PATH_DATA/participants.json .
+fi
+
+if [[ ! -f "README.md" ]]; then
+  rsync -avzh $PATH_DATA/README.md .
+fi
+
+if [[ ! -f "dataset_description.tsv" ]]; then
+  rsync -avzh $PATH_DATA/dataset_description .
+fi
+
+# Copy source images
+rsync -avzh $PATH_DATA/$SUBJECT .
+
+#copy derivatives
+rsync -avzh $PATH_DATA/derivatives .
+
+# Script starts here
+cd ${SUBJECT}/func
+file_bold=${SUBJECT}_task-rest_bold
+file_bold_seg=${PATH_DATA}/derivatives/labels/${SUBJECT}/func/${SUBJECT}_task-rest_bold_seg-manual
+
+sct_register_multimodal -i ${file_bold}.nii.gz -d ${file_bold_seg}.nii.gz -o ${file_bold}_to_${file_bold}_reg.nii.gz -identity 0
+rm warp_${SUBJECT}_task-rest_bold_seg-manual2${SUBJECT}_task-rest_bold.nii.gz warp_${SUBJECT}_task-rest_bold2${SUBJECT}_task-rest_bold_seg-manual.nii.gz ${SUBJECT}_task-rest_bold.nii.gz
+mv ${file_bold}_to_${file_bold}_reg.nii.gz ${file_bold}.nii.gz