working on a large UNET3D that worked fine with input samples of shape (batch_n,1,64,64,32).
now i switch to a  new dataset with different sample shape - (batch_n,1,79,95,68)
getting an error during concatenation of skip connection caused by dimension mismatch.
i’m pretty sure the root of the error is in the fact there’s a downsample (by setting stride=2) of an odd nubmer and then upsample which causes a discrepency. when shape was 64,64,32 the division by 2 was always coordinated with the upsample by 2.
so far i couldn’t find a solution so hoping someone might have come across a similar issue in the past and can share an insight.
p.s
i tried simply turning the odd shape into an even one, like (batch_n,1,78,94,68) but still getting the same error. i guess i had luck with the original shape that is dividing nicely by 2
here’s the code:
import torch.nn as nn
import torch
from torchsummary import summary
import torchsummaryX
from lib.medzoo.BaseModelClass import BaseModel


class UNet3D_inpainting(BaseModel):
    """
    Implementations based on the Unet3D paper: https://arxiv.org/abs/1606.06650
    with changes to fit volume inpainting
    """

    def __init__(self, in_channels, n_classes, args, base_n_filter=8):
        super(UNet3D_inpainting, self).__init__()
        self.n_classes = n_classes # no classification, just regression
        self.in_channels = in_channels
        self.n_subjects = args.subject_num
        self.dim = args.dim
        self.base_n_filter = base_n_filter
        self.lrelu = nn.LeakyReLU()
        self.dropout3d = nn.Dropout3d(p=args.dropout[0])
        self.upsacle = nn.Upsample(scale_factor=2, mode='nearest')
        self.softmax = nn.Softmax(dim=1)
        self.context0 = int(args.context_0)
        self.conv3d_c1_1 = nn.Conv3d(self.in_channels, self.base_n_filter, kernel_size=3, stride=1, padding=1,
                                     bias=False)
        self.conv3d_c1_2 = nn.Conv3d(self.base_n_filter, self.base_n_filter, kernel_size=3, stride=1, padding=1,
                                     bias=False)
        self.lrelu_conv_c1 = self.lrelu_conv(self.base_n_filter, self.base_n_filter)
        self.inorm3d_c1 = nn.InstanceNorm3d(self.base_n_filter)

        self.conv3d_c2 = nn.Conv3d(self.base_n_filter, self.base_n_filter * 2, kernel_size=3, stride=2, padding=1,
                                   bias=False)
        self.norm_lrelu_conv_c2 = self.norm_lrelu_conv(self.base_n_filter * 2, self.base_n_filter * 2)
        self.inorm3d_c2 = nn.InstanceNorm3d(self.base_n_filter * 2)

        self.conv3d_c3 = nn.Conv3d(self.base_n_filter * 2, self.base_n_filter * 4, kernel_size=3, stride=2, padding=1,
                                   bias=False)
        self.norm_lrelu_conv_c3 = self.norm_lrelu_conv(self.base_n_filter * 4, self.base_n_filter * 4)
        self.inorm3d_c3 = nn.InstanceNorm3d(self.base_n_filter * 4)

        self.conv3d_c4 = nn.Conv3d(self.base_n_filter * 4, self.base_n_filter * 8, kernel_size=3, stride=2, padding=1,
                                   bias=False)
        self.norm_lrelu_conv_c4 = self.norm_lrelu_conv(self.base_n_filter * 8, self.base_n_filter * 8)
        self.inorm3d_c4 = nn.InstanceNorm3d(self.base_n_filter * 8)

        self.conv3d_c5 = nn.Conv3d(self.base_n_filter * 8, self.base_n_filter * 16, kernel_size=3, stride=2, padding=1,
                                   bias=False)
        self.norm_lrelu_conv_c5 = self.norm_lrelu_conv(self.base_n_filter * 16, self.base_n_filter * 16)
        self.norm_lrelu_upscale_conv_norm_lrelu_l0 = self.norm_lrelu_upscale_conv_norm_lrelu(self.base_n_filter * 16,
                                                                                             self.base_n_filter * 8)

        self.conv3d_l0 = nn.Conv3d(self.base_n_filter * 8, self.base_n_filter * 8, kernel_size=1, stride=1, padding=0,
                                   bias=False)
        self.inorm3d_l0 = nn.InstanceNorm3d(self.base_n_filter * 8)

        self.conv_norm_lrelu_l1 = self.conv_norm_lrelu(self.base_n_filter * 16, self.base_n_filter * 16)
        self.conv3d_l1 = nn.Conv3d(self.base_n_filter * 16, self.base_n_filter * 8, kernel_size=1, stride=1, padding=0,
                                   bias=False)
        self.norm_lrelu_upscale_conv_norm_lrelu_l1 = self.norm_lrelu_upscale_conv_norm_lrelu(self.base_n_filter * 8,
                                                                                             self.base_n_filter * 4)

        self.conv_norm_lrelu_l2 = self.conv_norm_lrelu(self.base_n_filter * 8, self.base_n_filter * 8)
        self.conv3d_l2 = nn.Conv3d(self.base_n_filter * 8, self.base_n_filter * 4, kernel_size=1, stride=1, padding=0,
                                   bias=False)
        self.norm_lrelu_upscale_conv_norm_lrelu_l2 = self.norm_lrelu_upscale_conv_norm_lrelu(self.base_n_filter * 4,
                                                                                             self.base_n_filter * 2)

        self.conv_norm_lrelu_l3 = self.conv_norm_lrelu(self.base_n_filter * 4, self.base_n_filter * 4)
        self.conv3d_l3 = nn.Conv3d(self.base_n_filter * 4, self.base_n_filter * 2, kernel_size=1, stride=1, padding=0,
                                   bias=False)
        self.norm_lrelu_upscale_conv_norm_lrelu_l3 = self.norm_lrelu_upscale_conv_norm_lrelu(self.base_n_filter * 2,
                                                                                             self.base_n_filter)

        self.conv_norm_lrelu_l4 = self.conv_norm_lrelu(self.base_n_filter * 2, self.base_n_filter * 2)
        self.conv3d_l4 = nn.Conv3d(self.base_n_filter * 2, self.n_classes, kernel_size=1, stride=1, padding=0,
                                   bias=False)

        self.ds2_1x1_conv3d = nn.Conv3d(self.base_n_filter * 8, self.n_classes, kernel_size=1, stride=1, padding=0,
                                        bias=False)
        self.ds3_1x1_conv3d = nn.Conv3d(self.base_n_filter * 4, self.n_classes, kernel_size=1, stride=1, padding=0,
                                        bias=False)

    def conv_norm_lrelu(self, feat_in, feat_out):
        return nn.Sequential(
            nn.Conv3d(feat_in, feat_out, kernel_size=3, stride=1, padding=1, bias=False),
            nn.InstanceNorm3d(feat_out),
            nn.LeakyReLU())

    def norm_lrelu_conv(self, feat_in, feat_out):
        return nn.Sequential(
            nn.InstanceNorm3d(feat_in),
            nn.LeakyReLU(),
            nn.Conv3d(feat_in, feat_out, kernel_size=3, stride=1, padding=1, bias=False))

    def lrelu_conv(self, feat_in, feat_out):
        return nn.Sequential(
            nn.LeakyReLU(),
            nn.Conv3d(feat_in, feat_out, kernel_size=3, stride=1, padding=1, bias=False))

    def norm_lrelu_upscale_conv_norm_lrelu(self, feat_in, feat_out):
        return nn.Sequential(
            nn.InstanceNorm3d(feat_in),
            nn.LeakyReLU(),
            nn.Upsample(scale_factor=2, mode='nearest'),
            # should be feat_in*2 or feat_in
            nn.Conv3d(feat_in, feat_out, kernel_size=3, stride=1, padding=1, bias=False),
            nn.InstanceNorm3d(feat_out),
            nn.LeakyReLU())

    def forward(self, x, subj):

        #  Level 1 context pathway
        context_0 = x
        out = self.conv3d_c1_1(x)
        residual_1 = out
        out = self.lrelu(out)
        out = self.conv3d_c1_2(out)
        out = self.dropout3d(out)
        out = self.lrelu_conv_c1(out)
        # Element Wise Summation
        out += residual_1
        context_1 = self.lrelu(out)
        out = self.inorm3d_c1(out)
        out = self.lrelu(out)
        # Level 2 context pathway
        out = self.conv3d_c2(out)
        residual_2 = out
        out = self.norm_lrelu_conv_c2(out)
        out = self.dropout3d(out)
        out = self.norm_lrelu_conv_c2(out)
        out += residual_2
        out = self.inorm3d_c2(out)
        out = self.lrelu(out)
        context_2 = out
        # Level 3 context pathway
        out = self.conv3d_c3(out)
        residual_3 = out
        out = self.norm_lrelu_conv_c3(out)
        out = self.dropout3d(out)
        out = self.norm_lrelu_conv_c3(out)
        out += residual_3
        out = self.inorm3d_c3(out)
        out = self.lrelu(out)
        context_3 = out
        # Level 4 context pathway
        out = self.conv3d_c4(out)
        residual_4 = out
        out = self.norm_lrelu_conv_c4(out)
        out = self.dropout3d(out)
        out = self.norm_lrelu_conv_c4(out)
        out += residual_4
        out = self.inorm3d_c4(out)
        out = self.lrelu(out)
        context_4 = out
        # Level 5
        out = self.conv3d_c5(out)
        residual_5 = out
        out = self.norm_lrelu_conv_c5(out)
        out = self.dropout3d(out)
        out = self.norm_lrelu_conv_c5(out)
        out += residual_5
        out = self.norm_lrelu_upscale_conv_norm_lrelu_l0(out)
        out = self.conv3d_l0(out)
        out = self.inorm3d_l0(out)
        out = self.lrelu(out)

        # Level 1 localization pathway
        out = torch.cat([out, context_4], dim=1)
        out = self.conv_norm_lrelu_l1(out)
        out = self.conv3d_l1(out)
        out = self.norm_lrelu_upscale_conv_norm_lrelu_l1(out)
        # Level 2 localization pathway
      
        out = torch.cat([out, context_3], dim=1)
        out = self.conv_norm_lrelu_l2(out)
        ds2 = out
        out = self.conv3d_l2(out)
        out = self.norm_lrelu_upscale_conv_norm_lrelu_l2(out)


        # Level 3 localization pathway
        out = torch.cat([out, context_2], dim=1)
        out = self.conv_norm_lrelu_l3(out)
        ds3 = out
        out = self.conv3d_l3(out)
        out = self.norm_lrelu_upscale_conv_norm_lrelu_l3(out)

        #('level 3 - localize - shape ', out.shape)

        # Level 4 localization pathway
        out = torch.cat([out, context_1], dim=1)
        out = self.conv_norm_lrelu_l4(out)
        out_pred = self.conv3d_l4(out)
        ds2_1x1_conv = self.ds2_1x1_conv3d(ds2)
        ds1_ds2_sum_upscale = self.upsacle(ds2_1x1_conv)
        ds3_1x1_conv = self.ds3_1x1_conv3d(ds3)
        ds1_ds2_sum_upscale_ds3_sum = ds1_ds2_sum_upscale + ds3_1x1_conv
        ds1_ds2_sum_upscale_ds3_sum_upscale = self.upsacle(ds1_ds2_sum_upscale_ds3_sum)

        out = out_pred + ds1_ds2_sum_upscale_ds3_sum_upscale
        seg_layer = out + self.context0 * context_0
        return seg_layer