diff --git a/b0realsim/label_to_chi.py b/b0realsim/label_to_chi.py
index 6137ad8..f1499d1 100644
--- a/b0realsim/label_to_chi.py
+++ b/b0realsim/label_to_chi.py
@@ -6,36 +6,13 @@
 import json
 import datetime
 import git
-
+from utils.tissue2MR import run_tissue2MR
 
 def label_to_chi(bids_subject_dir):
 
     bids_subject_dir = Path(bids_subject_dir)
     subject = str(bids_subject_dir.stem)
-    merged_labels_path = bids_subject_dir / ".." / 'derivatives' / 'labels' / subject / 'anat' / (subject + '_T1w_label-all.nii.gz')
-    
-
-    vol = nib.load(merged_labels_path.resolve())
-
-    vol_data = vol.get_fdata()
-
-    vol_data.astype(np.float64)
-
-    vol_data[vol_data==0] = 0.35
-    vol_data[vol_data==1] = -9.05
-    vol_data[vol_data==2] = -2
-    vol_data[vol_data==3] = -2
-    vol_data[vol_data==4] = -4.2
-    vol_data[vol_data==5] = -4.2
-    vol_data[vol_data==6] = -4.2
-    vol_data[vol_data==56] = -9.04
-    vol_data[vol_data==60] = -9.05
-    vol_data[vol_data==91] = -11
-    vol_data[vol_data==92] = -11
-    vol_data[vol_data==93] = -9.055
-    vol_data[vol_data==100] = -9.055
-
-    new_volume = nib.Nifti1Image(vol_data, vol.affine, vol.header,  dtype=np.float64)
+    merged_labels_path = bids_subject_dir / ".." / 'derivatives' /'labels' / subject / 'anat' / (subject + '_T1w_label-all.nii.gz')
 
     # Check if the directory  bids_subject_dir / ".." / 'derivatives' / subject / exists and if no, create it
 
@@ -47,9 +24,16 @@ def label_to_chi(bids_subject_dir):
     if not os.path.exists(bids_subject_dir / ".." / 'derivatives' / subject / 'anat' ):
         os.makedirs(bids_subject_dir / ".." / 'derivatives' / subject / 'anat' )
     
-    chi_file = bids_subject_dir / ".." / 'derivatives' / subject / 'anat' / (subject + '_T1w-chi.nii.gz')
+    chi_file = bids_subject_dir / ".." / 'derivatives' / 'b0sim' /subject / 'anat' / (subject + '_T1w-chi.nii.gz')
 
-    nib.save(new_volume, chi_file)
+    vol = nib.load(merged_labels_path.resolve())
+    run_tissue2MR(
+        in_file = str(merged_labels_path.resolve()),
+        seg_tool = "compare_fm",
+        version = "ds005616",
+        tissue_prop = "sus",
+        out_file = str(chi_file)
+    )
 
     # Save json
 
@@ -65,48 +49,8 @@ def label_to_chi(bids_subject_dir):
     bids_sidecar['input file'] = str(merged_labels_path.resolve())
     bids_sidecar['command'] = 'python label_to_chi.py -s ' + str(bids_subject_dir)
 
-    bids_sidecar['anatomy'] = {}
-    bids_sidecar['anatomy']['background'] = {}
-    bids_sidecar['anatomy']['background']['label'] = 0
-    bids_sidecar['anatomy']['background']['chi'] = 0.35
-    bids_sidecar['anatomy']['body'] = {}
-    bids_sidecar['anatomy']['body']['label'] = '1'
-    bids_sidecar['anatomy']['body']['chi'] = -9.05
-    bids_sidecar['anatomy']['sinus'] = {}
-    bids_sidecar['anatomy']['sinus'] ['label'] = 2
-    bids_sidecar['anatomy']['sinus'] ['chi'] = -2
-    bids_sidecar['anatomy']['earcanal'] = {}
-    bids_sidecar['anatomy']['earcanal'] ['label'] = 3
-    bids_sidecar['anatomy']['earcanal']['chi'] = -2
-    bids_sidecar['anatomy']['trachea'] = {}
-    bids_sidecar['anatomy']['trachea']['label'] = 4
-    bids_sidecar['anatomy']['trachea']['chi'] = -4.2
-    bids_sidecar['anatomy']['rightlung'] = {}
-    bids_sidecar['anatomy']['rightlung']['label'] = 5
-    bids_sidecar['anatomy']['rightlung']['chi'] = -4.2
-    bids_sidecar['anatomy']['leftlung'] = {}
-    bids_sidecar['anatomy']['leftlung']['label'] = 6
-    bids_sidecar['anatomy']['leftlung']['chi'] = -4.2
-    bids_sidecar['anatomy']['brain'] = {}
-    bids_sidecar['anatomy']['brain']['label'] = 56
-    bids_sidecar['anatomy']['brain']['chi'] = -9.04
-    bids_sidecar['anatomy']['eyes'] = {}
-    bids_sidecar['anatomy']['eyes']['label'] = 60
-    bids_sidecar['anatomy']['eyes']['chi'] = -9.05
-    bids_sidecar['anatomy']['skull'] = {}
-    bids_sidecar['anatomy']['skull']['label'] = 91
-    bids_sidecar['anatomy']['skull']['chi'] = -11
-    bids_sidecar['anatomy']['verterbae'] = {}
-    bids_sidecar['anatomy']['verterbae']['label'] = 92
-    bids_sidecar['anatomy']['verterbae']['chi'] = -11
-    bids_sidecar['anatomy']['disks'] = {}
-    bids_sidecar['anatomy']['disks']['label'] = 93
-    bids_sidecar['anatomy']['disks']['chi'] = -9.055
-    bids_sidecar['anatomy']['canal'] = {}
-    bids_sidecar['anatomy']['canal']['label'] = 100
-    bids_sidecar['anatomy']['canal']['chi'] = -9.055
-
-    json_file = bids_subject_dir / ".." / 'derivatives' / subject / 'anat' / (subject + '_T1w-chi.json')
+
+    json_file = bids_subject_dir / ".." / 'derivatives' / 'b0sim' /subject / 'anat' / (subject + '_T1w-chi.json')
     if os.path.exists(json_file):
         os.remove(json_file)
 
diff --git a/b0realsim/label_to_perm_cond.py b/b0realsim/label_to_perm_cond.py
new file mode 100644
index 0000000..3a8fdc8
--- /dev/null
+++ b/b0realsim/label_to_perm_cond.py
@@ -0,0 +1,90 @@
+import nibabel as nib
+import numpy as np
+import argparse
+from pathlib import Path
+import os
+import json
+import datetime
+import git
+from utils.tissue2MR import run_tissue2MR
+
+
+def label_to_perm_cond(bids_subject_dir):
+
+    bids_subject_dir = Path(bids_subject_dir)
+    subject = str(bids_subject_dir.stem)
+    merged_labels_path = bids_subject_dir / ".." / 'derivatives' / 'labels' / subject / 'anat' / (subject + '_T1w_label-all.nii.gz')
+
+    # Check if the directory  bids_subject_dir / ".." / 'derivatives' / subject / exists and if no, create it
+
+    if not os.path.exists(bids_subject_dir / ".." / 'derivatives' / subject ):
+        os.makedirs(bids_subject_dir / ".." / 'derivatives' / subject )
+
+    # Check if the directory  bids_subject_dir / ".." / 'derivatives' / subject / 'anat' exists and if no, create it
+
+    if not os.path.exists(bids_subject_dir / ".." / 'derivatives' / subject / 'anat' ):
+        os.makedirs(bids_subject_dir / ".." / 'derivatives' / subject / 'anat' )
+
+    elecsim_anat_dir = bids_subject_dir / ".." / 'derivatives' / 'elecsim' / subject / 'anat'
+    os.makedirs(elecsim_anat_dir, exist_ok=True)
+
+    perm7t_file = bids_subject_dir / ".." / 'derivatives' / 'elecsim' / subject / 'anat' / (subject + '_T1w-perm7T.nii.gz')
+    chi7t_file = bids_subject_dir / ".." / 'derivatives' / 'elecsim' / subject / 'anat' / (subject + '_T1w-cond7T.nii.gz')
+
+    run_tissue2MR(
+        in_file = str(merged_labels_path.resolve()),
+        seg_tool = "compare_fm",
+        version = "ds005616",
+        tissue_prop = "perm7T",
+        out_file = str(perm7t_file)
+    )
+
+    run_tissue2MR(
+        in_file = str(merged_labels_path.resolve()),
+        seg_tool = "compare_fm",
+        version = "ds005616",
+        tissue_prop = "cond7T",
+        out_file = str(chi7t_file)
+    )
+    # Save json
+
+    repo = git.Repo(search_parent_directories=True)
+
+
+    bids_sidecar = {}
+    bids_sidecar['author'] = os.getenv('USERNAME')
+    bids_sidecar['date'] = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
+    bids_sidecar['script'] = str(Path(os.path.abspath(__file__)).resolve())
+    bids_sidecar['script source'] = repo.remotes.origin.url
+    bids_sidecar['script commit hash'] = repo.head.object.hexsha
+    bids_sidecar['input file'] = str(merged_labels_path.resolve())
+    bids_sidecar['command'] = 'python label_to_perm_cond.py -s ' + str(bids_subject_dir)
+
+    json_perm7t_file = bids_subject_dir / ".." / 'derivatives' / subject / 'anat' / (subject + '_T1w-perm7T.json')
+    json_cond7t_file = bids_subject_dir / ".." / 'derivatives' / subject / 'anat' / (subject + '_T1w-cond7T.json')
+    if os.path.exists(json_perm7t_file):
+        os.remove(json_perm7t_file)
+
+    with open(json_perm7t_file, 'w', encoding='utf-8') as f:
+        json.dump(bids_sidecar, f, ensure_ascii=False, indent=4)
+
+    if os.path.exists(json_cond7t_file):
+        os.remove(json_cond7t_file)
+
+    with open(json_cond7t_file, 'w', encoding='utf-8') as f:
+        json.dump(bids_sidecar, f, ensure_ascii=False, indent=4)
+
+
+if __name__ == "__main__":
+    
+    current_directory = os.path.dirname(os.path.abspath(__file__))
+
+    # Create an argument parser
+    parser = argparse.ArgumentParser(description="Process subject directory path and other arguments.")
+    
+    # Add the -s argument to the parser
+    parser.add_argument("-s", "--bids_subject_dir", required=True, help="Path to the subject directory in BIDS format")
+
+    # Parse the arguments
+    args = parser.parse_args()
+    label_to_perm_cond(args.bids_subject_dir)
diff --git a/b0realsim/step_2_1_generate_perm_cond.sh b/b0realsim/step_2_1_generate_perm_cond.sh
new file mode 100755
index 0000000..e2d9517
--- /dev/null
+++ b/b0realsim/step_2_1_generate_perm_cond.sh
@@ -0,0 +1,89 @@
+#!/bin/bash
+
+# Find all the subjects in the bids directory and create a list of them
+# This is useful for the batch processing of subjects
+
+# Parse the command line arguments -b --bids_dir
+while getopts ":b:" opt; do
+  case ${opt} in
+    b )
+      BIDS_DIR=$OPTARG
+      ;;
+    \? )
+      echo "Usage: cmd [-b] bids_dir"
+      exit 1
+      ;;
+  esac
+done
+
+# Handle Windows-style paths like E:/... or C:/...
+if [[ "$BIDS_DIR" =~ ^[A-Z]:/ ]]; then
+    drive=$(echo $BIDS_DIR | cut -c1 | tr 'A-Z' 'a-z')
+    path=$(echo $BIDS_DIR | cut -c3-)
+    BIDS_DIR="/cygdrive/$drive/$path"
+fi
+
+# Print the bids directory to the screen
+echo "BIDS directory: $BIDS_DIR"
+
+# Check if BIDS_DIR exists
+if [ ! -d "$BIDS_DIR" ]; then
+    echo "[ERROR] BIDS directory not found: $BIDS_DIR"
+    exit 1
+fi
+
+# If subjects.txt exists, remove it and create a new one
+if [ -f subjects.txt ]; then
+    rm subjects.txt
+    touch subjects.txt
+fi
+
+# Find all the subjects in the bids directory
+SUBJECTS=$(ls $BIDS_DIR | grep sub-)
+
+# Remove sub-unfErssm001 and sub-unfErssm021 from the list of subjects
+SUBJECTS=$(echo $SUBJECTS | sed 's/sub-unfErssm001//g' | sed 's/sub-unfErssm021//g')
+
+echo "Subjects found:"
+echo $SUBJECTS
+
+# Create a list of the subjects
+echo $SUBJECTS > subjects.txt
+
+# Get script directory
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
+# Convert DIR to Windows path for Windows Python
+WIN_DIR=$(echo "$DIR" | sed 's|/cygdrive/\([a-z]\)/|\U\1:/|')
+
+for subject in $SUBJECTS
+do
+    # Skip empty entries from excluded subjects
+    if [ -z "$subject" ]; then
+        continue
+    fi
+
+    echo "[INFO] Processing $subject"
+
+    # Convert BIDS_DIR to Windows path
+    WIN_BIDS_DIR=$(echo "$BIDS_DIR" | sed 's|/cygdrive/\([a-z]\)/|\U\1:/|')
+
+    # Check if subject folder exists
+    if [ ! -d "$WIN_BIDS_DIR/$subject" ]; then
+        echo "[WARNING] Subject folder not found: $WIN_BIDS_DIR/$subject, skipping..."
+        continue
+    fi
+
+    # Check if Python script exists
+    if [ ! -f "$WIN_DIR/label_to_perm_cond.py" ]; then
+        echo "[ERROR] Python script not found: $WIN_DIR/label_to_perm_cond.py"
+        exit 1
+    fi
+
+    # Run Python to generate perm/cond maps
+    "C:/Users/Admin/Miniconda3/python.exe" "$WIN_DIR/label_to_perm_cond.py" -s "$WIN_BIDS_DIR/$subject"
+done
+
+echo "[INFO] All subjects processed."
+
+
diff --git a/b0realsim/utils/__init__.py b/b0realsim/utils/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/b0realsim/utils/tissue2MR.py b/b0realsim/utils/tissue2MR.py
new file mode 100644
index 0000000..0cee772
--- /dev/null
+++ b/b0realsim/utils/tissue2MR.py
@@ -0,0 +1,46 @@
+import subprocess
+from pathlib import Path
+
+def run_tissue2MR(
+    in_file: str,
+    seg_tool: str,
+    version: str,
+    tissue_prop: str,
+    out_file: str,
+):
+    """
+    Run tissue_to_MR from command line inside Python.
+
+    Parameters
+    ----------
+    in_file : str
+        Path to input NIfTI file (.nii.gz).
+    seg_tool : str
+        The tool used to segmented the input file (argument to -s).
+    version : str
+        Version of the tool used to select approriate dictionary (argument to -v).
+    tissue_prop : str
+        Tissue type desired (argument to -t).
+    out_file : str
+        Path to output NIfTI file (.nii.gz).
+    """
+
+    # Ensure paths are safe
+    in_file = Path(in_file).resolve()
+    out_file = Path(out_file).resolve()
+
+    cmd = [
+        "tissue_to_MR",
+        "-i", str(in_file),
+        "-s", seg_tool,
+        "-v", version,
+        "-t", tissue_prop,
+        "-o", str(out_file)
+    ]
+
+    try:
+        subprocess.run(cmd, check=True)
+        print(f"[INFO] tissue_to_MR finished successfully. Output: {out_file}")
+    except subprocess.CalledProcessError as e:
+        print("[ERROR] tissue_to_MR failed!")
+        print(e)