correct phaseEncoding issues & automate visualization and file renaming & combine echos

Author: Monika_Utrosa_Skerjanec

build_singularity_img.sh

@@ -0,0 +1,2 @@
+# Build singularity image
+singularity build /my_images/fmriprep-25.2.3.simg docker://poldracklab/fmriprep:25.2.3

correct_PED.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python3
+# Time-stamp: <02-12-2025 m.utrosa@bcbl.eu>
+import json
+from bids import BIDSLayout
+from pathlib import Path
+
+bids_root = "/home/mutrosa/Documents/projects/select_fMRI/data_MRI/sourcedata/raw"
+
+# Initialize BIDS layout
+layout = BIDSLayout(bids_root, validate=False)
+
+# Get json files of single-band reference images
+sbref_files = layout.get(suffix='sbref', extension='.json', return_type='filename')
+print(f"Found {len(sbref_files)} sbref files.")
+
+for sbref_path in sbref_files:
+
+    # Identify the run number from file metadata
+    entities = layout.parse_file_entities(sbref_path)
+    run = entities.get("run", None)
+    if run != "02" and run != 2:
+        continue
+    
+    with open(sbref_path, 'r') as f:
+        meta = json.load(f)
+
+    # Modify PED only if it is exactly "j-"
+    if meta.get("PhaseEncodingDirection") == "j-":
+        meta["PhaseEncodingDirection"] = "i"
+        with open(sbref_path, 'w') as f:
+            json.dump(meta, f, indent=4)
+        print(f"Updated PED in: {sbref_path}")
+    else:
+        print(f"Skipping {sbref_path}: PED is {meta.get('PhaseEncodingDirection')}")

fMRIprep_localizer.sh

@@ -7,18 +7,21 @@ set -eo pipefail
 # Running the code in an environment specific to the project
 source activate localizer_fMRI
 
-# Activate the correct conda environment: conda activate dcm2bids
-subID="01"
-
 # STEP 0
 ## Curate the data automatically and manually (remove bad runs).
 ## Bad runs are runs that were interrupted due to participant's request (bathroom break, discomfort, ...),
 ## or a mistake while running the sequences (sound not coming through, response pad keys not working ...).
 
 # STEP 1
+## Identify the subject
+subID="01"
+
 ## Run the standard fMRIprep preprocessing pipeline.
-echo "Starting MRI preprocessing ..."
-bash data_MRI/code/preproc_singleSUB.sh "$subID" 
-echo "Completed STEP 1 ;)"
+echo "***** Starting MRI preprocessing for $subID *****"
+date
+bash data_MRI/code/preproc_singleSUB_docker.sh "$subID" 
+echo "***** Completed preprocessing for $subID ;) *****"
+date
 
-conda deactivate
+conda deactivate
+spd-say done

import_localizer.sh

@@ -1,5 +1,5 @@
 #! /usr/bin/env bash
-# Time-stamp: <2025-11-03 m.utrosa@bcbl.eu>
+# Time-stamp: <2025-12-09 m.utrosa@bcbl.eu>
 
 set -eo pipefail
 # -e => exits if any of the processes called generate a non-zero return code at the end.
@@ -10,12 +10,19 @@ source activate localizer_fMRI
 
 # Subject-specific parameters
 subID=1
-sesID=3
+sesID=1
+
+# Project-specific parameters
 project="SubCort_HighRes"
 task="localizer"
 homePath="/home/mutrosa/Documents/projects/select_fMRI"
-# acq_list=("DresdenNoFat" "DresdenWFat" "ME1TR880" "ME3TR1600" "ME3TR1100" "ME3TR850" "ME3TR700")
-acq_list=("DresdenNoFat175" "DresdenWFat175" "ME1TR780" "ME3TR1180" "ME3TR770" "ME3TR680")
+
+# Session-specific parameters
+if (( sesID == 1 )); then
+	acq_list=("DresdenNoFat" "DresdenWFat" "ME1TR880" "ME3TR1600" "ME3TR1100" "ME3TR850" "ME3TR700")
+else
+	acq_list=("DresdenNoFat175" "DresdenWFat175" "ME1TR780" "ME3TR1180" "ME3TR770" "ME3TR680")
+fi
 
 # STEP 0
 ## Generate sidecar files to set up the configuration files.
@@ -26,6 +33,7 @@ acq_list=("DresdenNoFat175" "DresdenWFat175" "ME1TR780" "ME3TR1180" "ME3TR770" "
 # c.) Removes noise from functional scans using NORDIC.
 echo "STEP 1: Starting curation of MRI data ..."
 python -m scripts.import.import_MRI "$subID" "$sesID" "$project" "$homePath" "${acq_list[@]}"
+python -m scripts.import.optimal_combo "$subID" "$sesID" "$task" "$homePath"
 echo "Completed STEP 1 ;)"
 
 # STEP 2: EVENTS
@@ -42,4 +50,5 @@ echo "STEP 3: Starting PHYSIO import..."
 python -m scripts.import.import_PHYSIO "$subID" "$sesID" "$project" "$task" "$homePath"
 echo "Completed STEP 3 ;)"
 
-conda deactivate
+conda deactivate
+spd-say done