diff --git a/PialNN/pialnn/1.0.0/config.py b/PialNN/pialnn/1.0.0/config.py
new file mode 100644
index 00000000..fc9a4c83
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/config.py
@@ -0,0 +1,33 @@
+import argparse
+    
+def load_config():
+
+    # args
+    parser = argparse.ArgumentParser(description="PialNN")
+    
+    # data
+    parser.add_argument('--data_path', default="./data/train/", type=str, help="path of the dataset")
+    parser.add_argument('--hemisphere', default="lh", type=str, help="left or right hemisphere (lh or rh)")
+    # model file
+    parser.add_argument('--model', help="path to best model")
+    #model
+    parser.add_argument('--nc', default=128, type=int, help="num of channels")
+    parser.add_argument('--K', default=5, type=int, help="kernal size")
+    parser.add_argument('--n_scale', default=3, type=int, help="num of scales for image pyramid")
+    parser.add_argument('--n_smooth', default=1, type=int, help="num of Laplacian smoothing layers")
+    parser.add_argument('--lambd', default=1.0, type=float, help="Laplacian smoothing weights")
+    # training
+    parser.add_argument('--train_data_ratio', default=0.8, type=float, help="percentage of training data")
+    parser.add_argument('--lr', default=1e-4, type=float, help="learning rate")
+    parser.add_argument('--n_epoch', default=200, type=int, help="total training epochs")
+    parser.add_argument('--ckpts_interval', default=10, type=int, help="save checkpoints after each n epoch")
+    parser.add_argument('--report_training_loss', default=True, type=bool, help="if report training loss")
+    parser.add_argument('--save_model', default=True, type=bool, help="if save training models")
+    parser.add_argument('--save_mesh_train', default=False, type=bool, help="if save mesh during training")
+    # evaluation
+    parser.add_argument('--save_mesh_eval', default=False, type=bool, help="if save mesh during evaluation")
+    parser.add_argument('--n_test_pts', default=150000, type=int, help="num of points sampled for evaluation")
+
+    config = parser.parse_args()
+
+    return config
diff --git a/PialNN/pialnn/1.0.0/data/dataload.py b/PialNN/pialnn/1.0.0/data/dataload.py
new file mode 100644
index 00000000..53c0cfc4
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/data/dataload.py
@@ -0,0 +1,105 @@
+import os
+import numpy as np
+import torch
+from tqdm import tqdm
+import nibabel as nib
+from torch.utils.data import Dataset
+
+
+"""
+volume: brain MRI volume
+v_in: vertices of input white matter surface
+f_in: faces of ground truth pial surface
+v_gt: vertices of input white matter surface
+f_gt: faces of ground truth pial surface
+"""
+
+class BrainData():
+    def __init__(self, volume, v_in, v_gt, f_in, f_gt):
+        self.v_in = torch.Tensor(v_in)
+        self.v_gt = torch.Tensor(v_gt)
+        self.f_in = torch.LongTensor(f_in)
+        self.f_gt = torch.LongTensor(f_gt)
+        self.volume = torch.Tensor(volume).unsqueeze(0)
+        
+        
+class BrainDataset(Dataset):
+    def __init__(self, data):
+        self.data = data
+
+    def __len__(self):
+        return len(self.data)
+
+    def __getitem__(self, i):
+        brain = self.data[i]
+        return brain.volume, brain.v_gt, \
+                brain.f_gt, brain.v_in, brain.f_in
+
+    
+def load_mri(path):
+    
+    brain = nib.load(path)
+    brain_arr = brain.get_fdata()
+    brain_arr = brain_arr / 255.
+    
+    # ====== change to your own transformation ======
+    # transpose and clip the data to [192,224,192]
+    brain_arr = brain_arr.transpose(1,2,0)
+    brain_arr = brain_arr[::-1,:,:]
+    brain_arr = brain_arr[:,:,::-1]
+    brain_arr = brain_arr[32:-32, 16:-16, 32:-32]
+    #================================================
+    
+    return brain_arr.copy()
+
+
+def load_surf(path):
+    v, f = nib.freesurfer.io.read_geometry(path)
+
+    # ====== change to your own transformation ======
+    # transpose and clip the data to [192,224,192]
+    v = v[:,[0,2,1]]
+    v[:,0] = v[:,0] - 32
+    v[:,1] = - v[:,1] - 15
+    v[:,2] = v[:,2] - 32
+
+    # normalize to [-1, 1]
+    v = v + 128
+    v = (v - [96, 112, 96]) / 112
+    f = f.astype(np.int32)
+    #================================================
+
+    return v, f
+    
+    
+def load_data(data_path, hemisphere):
+    """
+    data path: path of dataset
+    """
+    
+    subject_lists = sorted(os.listdir(data_path))
+
+    dataset = []
+    
+    for i in tqdm(range(len(subject_lists))):
+
+        subid = subject_lists[i]
+
+        # load brain MRI
+        volume = load_mri(data_path + subid + '/mri/orig.mgz')
+
+        # load ground truth pial surface
+        v_gt, f_gt = load_surf(data_path + subid + '/surf/' + hemisphere + '.pial')
+#         v_gt, f_gt = load_surf(data_path + subid + '/surf/' + hemisphere + '.pial.deformed')
+
+        # load input white matter surface
+        v_in, f_in = load_surf(data_path + subid + '/surf/' + hemisphere + '.white')
+#         v_in, f_in = load_surf(data_path + subid + '/surf/' + hemisphere + '.white.deformed')
+
+        braindata = BrainData(volume=volume, v_gt=v_gt, f_gt=f_gt,
+                              v_in=v_in, f_in=f_in)
+        dataset.append(braindata)
+
+    return dataset
+
+
diff --git a/PialNN/pialnn/1.0.0/data/test/example/mri/orig.mgz b/PialNN/pialnn/1.0.0/data/test/example/mri/orig.mgz
new file mode 100644
index 00000000..973eaadb
Binary files /dev/null and b/PialNN/pialnn/1.0.0/data/test/example/mri/orig.mgz differ
diff --git a/PialNN/pialnn/1.0.0/data/test/example/surf/lh.pial b/PialNN/pialnn/1.0.0/data/test/example/surf/lh.pial
new file mode 100644
index 00000000..b6bbff39
Binary files /dev/null and b/PialNN/pialnn/1.0.0/data/test/example/surf/lh.pial differ
diff --git a/PialNN/pialnn/1.0.0/data/test/example/surf/lh.white b/PialNN/pialnn/1.0.0/data/test/example/surf/lh.white
new file mode 100644
index 00000000..2d5a8a2d
Binary files /dev/null and b/PialNN/pialnn/1.0.0/data/test/example/surf/lh.white differ
diff --git a/PialNN/pialnn/1.0.0/data/train/SUBJECT_NAME/mri/mri_data_here.txt b/PialNN/pialnn/1.0.0/data/train/SUBJECT_NAME/mri/mri_data_here.txt
new file mode 100644
index 00000000..fa7cc9cb
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/data/train/SUBJECT_NAME/mri/mri_data_here.txt
@@ -0,0 +1 @@
+###
\ No newline at end of file
diff --git a/PialNN/pialnn/1.0.0/data/train/SUBJECT_NAME/surf/surface_data_here.txt b/PialNN/pialnn/1.0.0/data/train/SUBJECT_NAME/surf/surface_data_here.txt
new file mode 100644
index 00000000..fa7cc9cb
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/data/train/SUBJECT_NAME/surf/surface_data_here.txt
@@ -0,0 +1 @@
+###
\ No newline at end of file
diff --git a/PialNN/pialnn/1.0.0/docker/Dockerfile b/PialNN/pialnn/1.0.0/docker/Dockerfile
new file mode 100644
index 00000000..0b4df319
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/docker/Dockerfile
@@ -0,0 +1,51 @@
+FROM nvidia/cuda:12.2.0-devel-ubuntu20.04
+ENV LANG=C.UTF-8
+ENV LC_ALL=C.UTF-8
+ENV PATH=/opt/miniconda3/bin:$PATH
+ENV PYTHONDONTWRITEBYTECODE=1
+ENV PYTHONUNBUFFERED=1
+ENV PYTHONIOENCODING=UTF-8
+ENV PIPENV_VENV_IN_PROJECT=1
+ENV JCC_JDK=/usr/lib/jvm/java-8-openjdk-amd64
+RUN USE_CUDA=1
+RUN CUDA_VERSION=12.2.0
+RUN CUDNN_VERSION=8
+RUN LINUX_DISTRO=ubuntu
+RUN DISTRO_VERSION=20.04
+RUN TORCH_CUDA_ARCH_LIST="7.0 7.5 8.0 8.6"
+RUN rm -f /etc/apt/apt.conf.d/docker-clean; \
+echo 'Binary::apt::APT::Keep-Downloaded-Packages "true";' \
+> /etc/apt/apt.conf.d/keep-cache
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata && apt-get install -y --no-install-recommends \
+build-essential \
+ca-certificates \
+ccache \
+curl \
+git \
+wget \
+cmake \
+gfortran \
+libspatialindex-dev 
+RUN rm -rf /var/lib/apt/lists/*
+ENV PYTHON_VERSION=3.7
+ENV CONDA_URL=https://repo.anaconda.com/miniconda/Miniconda3-py37_4.10.3-Linux-x86_64.sh
+RUN curl -fsSL -v -o ~/miniconda.sh -O ${CONDA_URL} && \
+chmod +x ~/miniconda.sh && \
+~/miniconda.sh -b -p /opt/miniconda3 
+
+WORKDIR /app
+COPY pialnn.requirements.txt .
+COPY environment.yml .
+RUN conda env update -f environment.yml
+SHELL ["conda", "run", "-n", "base", "/bin/bash", "-c"]
+#RUN pip cache purge
+RUN pip install torch-scatter==latest+cu102 -f https://pytorch-geometric.com/whl/torch-1.7.0.html
+RUN pip install torch-sparse==latest+cu102 -f https://pytorch-geometric.com/whl/torch-1.7.0.html
+RUN pip install torch-cluster==latest+cu102 -f https://pytorch-geometric.com/whl/torch-1.7.0.html
+RUN pip install torch-spline-conv==latest+cu102 -f https://pytorch-geometric.com/whl/torch-1.7.0.html
+RUN pip install torch-geometric
+RUN pip install rtree
+RUN pip install -r pialnn.requirements.txt
+RUN conda install -c conda-forge libspatialindex=1.9.3
+RUN conda clean -a
+ENTRYPOINT ["/bin/bash", "-l", "-c"]
diff --git a/PialNN/pialnn/1.0.0/docker/environment.yml b/PialNN/pialnn/1.0.0/docker/environment.yml
new file mode 100644
index 00000000..322a1440
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/docker/environment.yml
@@ -0,0 +1,93 @@
+name: base
+channels:
+  - pytorch3d
+  - pytorch
+  - bottler
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=1_gnu
+  - blas=1.0=mkl
+  - ca-certificates=2022.9.24=ha878542_0
+  - certifi=2022.9.24=pyhd8ed1ab_0
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - cudatoolkit=10.2.89=hfd86e86_1
+  - dataclasses=0.8=pyhc8e2a94_3
+  - freetype=2.12.1=h4a9f257_0
+  - fvcore=0.1.5.post20220512=pyhd8ed1ab_0
+  - giflib=5.2.1=h7b6447c_0
+  - intel-openmp=2021.4.0=h06a4308_3561
+  - iopath=0.1.9=pyhd8ed1ab_0
+  - jpeg=9e=h7f8727e_0
+  - lcms2=2.12=h3be6417_0
+  - ld_impl_linux-64=2.38=h1181459_1
+  - lerc=3.0=h295c915_0
+  - libdeflate=1.8=h7f8727e_5
+  - libffi=3.3=he6710b0_2
+  - libgcc-ng=11.2.0=h1234567_1
+  - libgomp=11.2.0=h1234567_1
+  - libpng=1.6.37=hbc83047_0
+  - libspatialindex=1.9.3=h9c3ff4c_4
+  - libstdcxx-ng=11.2.0=h1234567_1
+  - libtiff=4.4.0=hecacb30_0
+  - libuv=1.40.0=h7b6447c_0
+  - libwebp=1.2.4=h11a3e52_0
+  - libwebp-base=1.2.4=h5eee18b_0
+  - lz4-c=1.9.3=h295c915_1
+  - mkl=2021.4.0=h06a4308_640
+  - mkl-service=2.4.0=py37h7f8727e_0
+  - mkl_fft=1.3.1=py37hd3c417c_0
+  - mkl_random=1.2.2=py37h51133e4_0
+  - ncurses=6.3=h5eee18b_3
+  - ninja=1.10.2=h06a4308_5
+  - ninja-base=1.10.2=hd09550d_5
+  - numpy=1.21.5=py37h6c91a56_3
+  - numpy-base=1.21.5=py37ha15fc14_3
+  - nvidiacub=1.10.0=0
+  - openssl=1.1.1s=h7f8727e_0
+  - pillow=9.2.0=py37hace64e9_1
+  - portalocker=2.6.0=py37h89c1867_0
+  - python=3.7.13=haa1d7c7_1
+  - python_abi=3.7=2_cp37m
+  - pytorch=1.7.0=py3.7_cuda10.2.89_cudnn7.6.5_0
+  - pytorch3d=0.6.2=py37_cu102_pyt170
+  - pyyaml=6.0=py37h540881e_4
+  - readline=8.2=h5eee18b_0
+  - setuptools=65.4.0=py37h06a4308_0
+  - six=1.16.0=pyhd3eb1b0_1
+  - sqlite=3.39.3=h5082296_0
+  - tabulate=0.9.0=pyhd8ed1ab_1
+  - termcolor=2.0.1=pyhd8ed1ab_1
+  - tk=8.6.12=h1ccaba5_0
+  - torchvision=0.8.1=py37_cu102
+  - tqdm=4.64.1=pyhd8ed1ab_0
+  - typing_extensions=4.3.0=py37h06a4308_0
+  - wheel=0.37.1=pyhd3eb1b0_0
+  - xz=5.2.6=h5eee18b_0
+  - yacs=0.1.8=pyhd8ed1ab_0
+  - yaml=0.2.5=h7f98852_2
+  - zlib=1.2.13=h5eee18b_0
+  - zstd=1.5.2=ha4553b6_0
+  - pip:
+    - charset-normalizer==2.1.1
+    - idna==3.4
+    - jinja2==3.1.2
+    - joblib==1.2.0
+    - markupsafe==2.1.1
+    - nvidia-ml-py3==7.352.0
+    - packaging==21.3
+    - pip==18.0
+    - pyparsing==3.0.9
+    - requests==2.28.1
+    - rtree==1.0.1
+    - scikit-learn==1.0.2
+    - scipy==1.7.3
+    - threadpoolctl==3.1.0
+    - torch-cluster==1.5.8
+    - torch-geometric==2.1.0.post1
+    - torch-scatter==2.0.5
+    - torch-sparse==0.6.8
+    - torch-spline-conv==1.2.0
+    - trimesh==3.15.8
+    - urllib3==1.26.12
diff --git a/PialNN/pialnn/1.0.0/docker/pialnn.requirements.txt b/PialNN/pialnn/1.0.0/docker/pialnn.requirements.txt
new file mode 100644
index 00000000..e6cb514b
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/docker/pialnn.requirements.txt
@@ -0,0 +1,47 @@
+certifi==2022.9.24
+charset-normalizer==2.1.1
+colorama==0.4.6
+dataclasses==0.8
+freesurfer-surface==2.0.0
+freetype-py==2.3.0
+fvcore==0.1.5.post20220512
+idna==3.3
+iopath==0.1.9
+Jinja2==3.1.2
+joblib==1.2.0
+MarkupSafe==2.1.1
+mkl-fft==1.3.1
+mkl-random==1.2.2
+mkl-service==2.4.0
+nibabel==3.2.1
+nilearn==0.8.1
+numpy==1.21.5
+nvidia-ml-py3==7.352.0
+packaging==21.3
+Pillow==9.2.0
+portalocker==2.6.0
+PyOpenGL==3.1.0
+pyparsing==3.0.9
+pyrender==0.1.45
+pytorch3d==0.6.2
+PyYAML==6.0
+requests==2.28.1
+Rtree==1.0.1
+scikit-learn==1.0.2
+scipy==1.7.3
+six==1.16.0
+tabulate==0.9.0
+termcolor==2.0.1
+threadpoolctl==3.1.0
+torch==1.7.0
+torch-cluster==1.5.8
+torch-geometric==2.1.0.post1
+torch-scatter==2.0.5
+torch-sparse==0.6.8
+torch-spline-conv==1.2.0
+torchvision==0.8.1
+tqdm==4.64.1
+trimesh==3.15.8
+typing-extensions==4.3.0
+urllib3==1.26.12
+yacs==0.1.8
diff --git a/PialNN/pialnn/1.0.0/example-data/sample.zip b/PialNN/pialnn/1.0.0/example-data/sample.zip
new file mode 120000
index 00000000..0b17fd67
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/example-data/sample.zip
@@ -0,0 +1 @@
+../../../../.git/annex/objects/XG/kw/MD5E-s9777720--5d02bc50297786ffde23197fe0db6e1b.zip/MD5E-s9777720--5d02bc50297786ffde23197fe0db6e1b.zip
\ No newline at end of file
diff --git a/PialNN/pialnn/1.0.0/model/pialnn.py b/PialNN/pialnn/1.0.0/model/pialnn.py
new file mode 100644
index 00000000..505e8bd8
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/model/pialnn.py
@@ -0,0 +1,201 @@
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+import numpy as np
+
+from utils import compute_normal
+
+
+"""
+Deformation Block
+nc: number of channels
+K: kernal size for local conv operation
+n_scale: num of layers of image pyramid
+"""
+
+class DeformBlock(nn.Module):
+    def __init__(self, nc=128, K=5, n_scale=3):
+        super(DeformBlock, self).__init__()
+
+        # mlp layers
+        self.fc1 = nn.Linear(6, nc)
+        self.fc2 = nn.Linear(nc*2, nc*4)
+        self.fc3 = nn.Linear(nc*4, nc*2)
+        self.fc4 = nn.Linear(nc*2, 3)
+
+        # for local convolution operation
+        self.localconv = nn.Conv3d(n_scale, nc, (K, K, K))
+        self.localfc = nn.Linear(nc, nc)
+        
+        self.n_scale = n_scale
+        self.nc = nc
+        self.K = K
+
+    def forward(self, v, f, volume):
+        
+        coord = v.clone()
+        normal = compute_normal(v, f)    # compute normal
+        
+        # point feature
+        x = torch.cat([v, normal], 2)
+        x = F.leaky_relu(self.fc1(x), 0.15)
+        
+        # local feature
+        cubes = self.cube_sampling(v, volume)    # extract K^3 cubes
+        x_local = self.localconv(cubes)
+        x_local = x_local.view(1, v.shape[1], self.nc)
+        x_local = self.localfc(x_local)
+
+        # fusion
+        x = torch.cat([x, x_local], 2)
+        x = F.leaky_relu(self.fc2(x), 0.15)
+        x = F.leaky_relu(self.fc3(x), 0.15)
+        x = torch.tanh(self.fc4(x)) * 0.1    # threshold the displacement
+
+        return coord + x    # v=v+dv
+
+    def initialize(self, L, W, H, device=None):
+        """initialize necessary constants"""
+        
+        LWHmax = max([L,W,H])
+        self.LWHmax = LWHmax
+        # rescale to [-1, 1]
+        self.rescale = torch.Tensor([L/LWHmax, W/LWHmax, H/LWHmax]).to(device)
+
+        # shape of mulit-scale image pyramid
+        self.pyramid_shape = torch.zeros([self.n_scale, 3]).to(device)
+        for i in range(self.n_scale):
+            self.pyramid_shape[i] = torch.Tensor([L/(2**i),
+                                                  W/(2**i),
+                                                  H/(2**i)]).to(device)
+        # for threshold
+        self.lower_bound = torch.tensor([(self.K-1)//2,
+                                         (self.K-1)//2,
+                                         (self.K-1)//2]).to(device)
+        # for storage of sampled cubes
+        self.cubes_holder = torch.zeros([1, self.n_scale,
+                                         self.K, self.K, self.K]).to(device)
+
+    def cube_sampling(self, v, volume):
+
+        # for storage of sampled cubes
+        cubes = self.cubes_holder.repeat(v.shape[1],1,1,1,1)
+
+        # 3D MRI volume
+        vol_ = volume.clone()
+        for n in range(self.n_scale):   # multi scales
+            if n > 0:
+                vol_ = F.avg_pool3d(vol_, 2)    # down sampling
+            vol = vol_[0,0]
+            
+            # find corresponding position
+            indices = (v[0] + self.rescale) * self.LWHmax / (2**(n+1))
+            indices = torch.round(indices).long()
+            indices = torch.max(torch.min(indices, self.pyramid_shape[n]-3),
+                                self.lower_bound).long()
+            
+            # sample values of each cube
+            for i in [-2,-1,0,1,2]:
+                for j in [-2,-1,0,1,2]:
+                    for k in [-2,-1,0,1,2]:
+                        cubes[:,n,2+i,2+j,2+k] = vol[indices[:,2]+i,
+                                                     indices[:,1]+j,
+                                                     indices[:,0]+k]
+        return cubes
+
+
+
+"""
+PialNN with 3 deformation blocks + 1 Laplacian smoothing layer
+"""
+
+class PialNN(nn.Module):
+    def __init__(self, nc=128, K=5, n_scale=3):
+        super(PialNN, self).__init__()
+        self.block1 = DeformBlock(nc, K, n_scale)
+        self.block2 = DeformBlock(nc, K, n_scale)
+        self.block3 = DeformBlock(nc, K, n_scale)
+        self.smooth = LaplacianSmooth(3, 3, aggr='mean')
+
+    def forward(self, v, f, volume, n_smooth=1, lambd=1.0):
+
+        x = self.block1(v, f, volume)
+        x = self.block2(x, f, volume)
+        x = self.block3(x, f, volume)
+        edge_list = torch.cat([f[0,:,[0,1]],
+                               f[0,:,[1,2]],
+                               f[0,:,[2,0]]], dim=0).transpose(1,0)
+        
+        for i in range(n_smooth):
+            x = self.smooth(x, edge_list, lambd=lambd)
+        
+        return x
+    
+    def initialize(self, L=256, W=256, H=256, device=None):
+        self.block1.initialize(L,W,H,device)
+        self.block2.initialize(L,W,H,device)
+        self.block3.initialize(L,W,H,device)
+
+
+
+"""
+LaplacianSmooth() is a differentiable Laplacian smoothing layer.
+The code is implemented based on the torch_geometric.nn.conv.GraphConv.
+For original GraphConv implementation, please see
+https://github.com/rusty1s/pytorch_geometric/blob/master/torch_geometric/nn/conv/graph_conv.py
+
+
+x: the coordinates of the vertices, (|V|, 3).
+edge_index: the list of edges, (2, |E|), e.g. [[0,1],[1,3],...]. 
+lambd: weight for Laplacian smoothing, between [0,1].
+out: the smoothed vertices, (|V|, 3).
+"""
+
+from typing import Union, Tuple
+from torch_geometric.typing import OptTensor, OptPairTensor, Adj, Size
+from torch import Tensor
+from torch_sparse import SparseTensor, matmul
+from torch_geometric.nn.conv import MessagePassing
+
+
+class LaplacianSmooth(MessagePassing):
+
+    def __init__(self, in_channels: Union[int, Tuple[int,
+                                                     int]], out_channels: int,
+                 aggr: str = 'add', bias: bool = True, **kwargs):
+        super(LaplacianSmooth, self).__init__(aggr=aggr, **kwargs)
+
+        self.in_channels = in_channels
+        self.out_channels = out_channels
+
+        if isinstance(in_channels, int):
+            in_channels = (in_channels, in_channels)
+
+
+    def forward(self, x: Union[Tensor, OptPairTensor], edge_index: Adj,
+                edge_weight: OptTensor = None, size: Size = None, lambd=0.5) -> Tensor:
+
+        if isinstance(x, Tensor):
+            x: OptPairTensor = (x, x)
+
+        # propagate_type: (x: OptPairTensor, edge_weight: OptTensor)
+        out = self.propagate(edge_index, x=x, edge_weight=edge_weight,
+                             size=size)
+        out = lambd * out 
+        x_r = x[1]
+        if x_r is not None:
+            out += (1-lambd) * x_r
+
+        return out
+
+
+    def message(self, x_j: Tensor, edge_weight: OptTensor) -> Tensor:
+        return x_j if edge_weight is None else edge_weight.view(-1, 1) * x_j
+
+    def message_and_aggregate(self, adj_t: SparseTensor,
+                              x: OptPairTensor) -> Tensor:
+        return matmul(adj_t, x[0], reduce=self.aggr)
+
+    def __repr__(self):
+        return '{}({}, {})'.format(self.__class__.__name__, self.in_channels,
+                                   self.out_channels)
diff --git a/PialNN/pialnn/1.0.0/model_card.yaml b/PialNN/pialnn/1.0.0/model_card.yaml
new file mode 100644
index 00000000..c70597d8
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/model_card.yaml
@@ -0,0 +1,33 @@
+Model_details:
+  Organization: DeepCSR
+  Model_date: t
+  Model_version: 1.0
+  Model_type: t
+  More_information: t
+  Citation_details: t
+  Contact_info: t
+Intended_use:
+  Primary_intended_uses: t
+  Primary_intended_users: t
+  Out_of_scope_use_cases: t
+Factors:
+  Relevant_factors: t
+  Evaluation_factors: t
+  Model_performance_measures: t
+Metrics:
+  Model Performance Measures: t
+  Decision Thresholds: t
+  Variation Approaches: t
+Evaluation Data:
+  Datasets: t
+  Motivation: t
+  Preprocessing: t
+Training Data:
+  Datasets: t
+  Motivation: t
+  Preprocessing: t
+Quantitative Analyses:
+  Unitary Results: t
+  Intersectional Results: t
+Ethical Considerations: t
+Caveats and Recommendations: t
diff --git a/PialNN/pialnn/1.0.0/predict.py b/PialNN/pialnn/1.0.0/predict.py
new file mode 100644
index 00000000..6b34b99c
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/predict.py
@@ -0,0 +1,106 @@
+import numpy as np
+from tqdm import tqdm
+
+import torch
+from torch.utils.data import DataLoader
+
+from config import load_config
+from data.dataload import load_data, BrainDataset
+from model.pialnn import PialNN
+from utils import compute_normal, save_mesh_obj, compute_distance
+
+
+if __name__ == '__main__':
+    
+    """set device"""
+    if torch.cuda.is_available():
+        device_name = "cuda:0"
+        print('selected gpu')
+    else:
+        device_name = "cpu"
+    device = torch.device(device_name)
+
+
+    """load configuration"""
+    config = load_config()
+
+    """load dataset"""
+    print("----------------------------")
+    print("Start loading dataset ...")
+    test_data = load_data(data_path = config.data_path,
+                          hemisphere = config.hemisphere)
+    n_data = len(test_data)
+    L,W,H = test_data[0].volume[0].shape  # shape of MRI
+    LWHmax = max([L,W,H])
+
+    test_set = BrainDataset(test_data)
+    testloader = DataLoader(test_set, batch_size=1, shuffle=True)
+    print("Finish loading dataset. There are total {} subjects.".format(n_data))
+    print("----------------------------")
+
+    
+    """load model"""
+    print("Start loading model ...")
+    model = PialNN(config.nc, config.K, config.n_scale).to(device)
+    model.load_state_dict(torch.load(config.model,
+                                     map_location=device))
+    model.initialize(L, W, H, device)
+    print("Finish loading model")
+    print("----------------------------")
+    
+    
+    """evaluation"""
+    print("Start evaluation ...")
+    with torch.no_grad():
+        #CD = []
+        #AD = []
+        #HD = []
+        for idx, data in tqdm(enumerate(testloader)):
+            volume_in, v_gt, f_gt, v_in, f_in = data
+
+            sub_id = idx
+	
+            volume_in = volume_in.to(device)
+            v_gt = v_gt.to(device)
+            f_gt = f_gt.to(device)
+            v_in = v_in.to(device)
+            f_in = f_in.to(device)
+
+            # set n_smooth > 1 if the mesh quality is not good
+            v_pred = model(v=v_in, f=f_in, volume=volume_in,
+                           n_smooth=config.n_smooth, lambd=config.lambd)
+
+            v_pred_eval = v_pred[0].cpu().numpy() * LWHmax/2 + [L/2,W/2,H/2]
+            f_pred_eval = f_in[0].cpu().numpy()
+            v_gt_eval = v_gt[0].cpu().numpy() * LWHmax/2 + [L/2,W/2,H/2]
+            f_gt_eval = f_gt[0].cpu().numpy()
+
+            # compute distance-based metrics
+            #cd, assd, hd = compute_distance(v_pred_eval, v_gt_eval,
+            #                                f_pred_eval, f_gt_eval, config.n_test_pts)
+            
+            #CD.append(cd)
+            #AD.append(assd)
+            #HD.append(hd)
+            print('sub_id',sub_id)
+            if config.save_mesh_eval:
+                path_save_mesh = "./pialnn_mesh_eval_"\
+                        +config.hemisphere+"_subject_"+str(sub_id)+".obj"
+
+                normal = compute_normal(v_pred, f_in)
+                n_pred_eval = normal[0].cpu().numpy()
+                save_mesh_obj(v_pred_eval, f_pred_eval, n_pred_eval, path_save_mesh)
+                
+                ################
+                path_save_mesh = "./pialnn_mesh_eval_"\
+                        +config.hemisphere+"_subject_"+str(sub_id)+"_gt.obj"
+
+                normal = compute_normal(v_gt, f_gt)
+                n_gt_eval = normal[0].cpu().numpy()
+                save_mesh_obj(v_gt_eval, f_gt_eval, n_gt_eval, path_save_mesh)
+
+    # print("CD: Mean={}, Std={}".format(np.mean(CD), np.std(CD)))
+    # print("AD: Mean={}, Std={}".format(np.mean(AD), np.std(AD)))
+    # print("HD: Mean={}, Std={}".format(np.mean(HD), np.std(HD)))
+    print("Finish evaluation.")
+    print("----------------------------")
diff --git a/PialNN/pialnn/1.0.0/spec.yaml b/PialNN/pialnn/1.0.0/spec.yaml
new file mode 100644
index 00000000..4e53730a
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/spec.yaml
@@ -0,0 +1,47 @@
+image:
+  docker: neuronets/deepcsr
+  singularity: nobrainer-zoo_deepcsr.sif
+repository:
+  repo_url: None
+  committish: None
+  repo_download: 'False'
+  repo_download_location: None
+inference:
+  prediction_script: trained-models/DeepCSR/deepcsr/1.0/predict.py
+  command: f"python {MODELS_PATH}/{model}/predict.py --conf_path {conf} --model_checkpoint
+    {infile[0]} --dataset {infile[1]}"
+  data_spec:
+    infile:
+      n_files: 1
+    outfile:
+      n_files: 1
+training_data_info:
+  data_number:
+    total: 1
+    train: 1
+    evaluate: 1
+    test: 1
+  biological_sex:
+    male: null
+    female: null
+  age_histogram: '1'
+  race: '1'
+  imaging_contrast_info: '1'
+  dataset_sources: '1'
+  data_sites:
+    number_of_sites: 1
+    sites: '1'
+  scanner_models: '1'
+  hardware: '1'
+  training_parameters:
+    input_shape: '1'
+    block_shape: '1'
+    n_classes: 1
+    lr: '1'
+    n_epochs: 1
+    total_batch_size: 1
+    number_of_gpus: 1
+    loss_function: '1'
+    metrics: '1'
+    data_preprocessing: '1'
+    data_augmentation: '1'
diff --git a/PialNN/pialnn/1.0.0/utils.py b/PialNN/pialnn/1.0.0/utils.py
new file mode 100644
index 00000000..90a83d10
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/utils.py
@@ -0,0 +1,61 @@
+import numpy as np
+import pytorch3d
+from pytorch3d.structures import Meshes
+import trimesh
+from trimesh.exchange.obj import export_obj
+from scipy.spatial import cKDTree
+
+
+def compute_normal(v, f):
+    """v, f: Tensors"""
+    normal = Meshes(verts=list(v),
+                    faces=list(f)).verts_normals_list()[0]
+    return normal.unsqueeze(0)
+
+
+def save_mesh_obj(v, f, n, path):
+    mesh_save = trimesh.Trimesh(vertices=v,
+                                faces=f,
+                                vertex_normals=n)
+    obj_save  = export_obj(mesh_save, include_normals=True)
+    with open(path, "w") as file:
+        print(obj_save, file=file)
+
+
+def compute_distance(v_pred, v_gt, f_pred, f_gt, n_samples=150000):
+    """
+    The results are evaluated based on three distances:
+    1. Chamfer Distance (CD)
+    2. Average Absolute Distance (AD)
+    3. Hausdorff Distance (HD)
+
+    Please see DeepCSR paper in details:
+    https://arxiv.org/abs/2010.11423
+    
+    For original code, please see:
+    https://bitbucket.csiro.au/projects/CRCPMAX/repos/deepcsr/browse/eval.py
+    """
+    
+    # chamfer distance
+    cd = 0
+    kdtree = cKDTree(v_pred)
+    cd += kdtree.query(v_gt)[0].mean()/2
+    kdtree = cKDTree(v_gt)
+    cd += kdtree.query(v_pred)[0].mean()/2
+
+    # AD & HD
+    mesh_pred = trimesh.Trimesh(vertices=v_pred, faces=f_pred)
+    pts_pred = mesh_pred.sample(n_samples)
+    mesh_gt = trimesh.Trimesh(vertices=v_gt, faces=f_gt)
+    pts_gt = mesh_gt.sample(n_samples)
+
+    _, P2G_dist, _ = trimesh.proximity.closest_point(mesh_pred, pts_gt)
+    _, G2P_dist, _ = trimesh.proximity.closest_point(mesh_gt, pts_pred)
+
+    # average absolute distance
+    assd = ((P2G_dist.sum() + G2P_dist.sum()) / float(P2G_dist.size + G2P_dist.size))
+    
+    # Hausdorff distance
+    hd = max(np.percentile(P2G_dist, 90), np.percentile(G2P_dist, 90))
+
+    return cd, assd, hd
\ No newline at end of file
diff --git a/PialNN/pialnn/1.0.0/weights/pialnn_model_lh_200epochs.pt b/PialNN/pialnn/1.0.0/weights/pialnn_model_lh_200epochs.pt
new file mode 120000
index 00000000..24fbebb2
--- /dev/null
+++ b/PialNN/pialnn/1.0.0/weights/pialnn_model_lh_200epochs.pt
@@ -0,0 +1 @@
+../../../../.git/annex/objects/Gk/wQ/MD5E-s3963107--e00fa887f4a16a3e726a614bfa62202d.pt/MD5E-s3963107--e00fa887f4a16a3e726a614bfa62202d.pt
\ No newline at end of file