fix bug for imcompartible B0 direction between SEPIA and LPCNN

kschan0214 · Oct 9, 2023 · 2937400 · 2937400
1 parent 9083249
commit 2937400
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Showing 7 changed files with 11 additions and 8 deletions.
diff --git a/addons/bfr/BFRnet/setup_BFRnet_environment.m b/addons/bfr/BFRnet/setup_BFRnet_environment.m
@@ -1,8 +1,8 @@
 %% This file specifies the Checkpoint of xQSM
 
 % Specify the directory of the xQSM code from Github
-deepMRI_HOME   	= '/project/3015069.05/bids/code/deepMRI/';
+deepMRI_HOME   	= '/home/common/matlab/sepia/external/deepMRI/';
 % If you have your own trained network, specify the file that contains the trained parameters
 % otherwise, uses the one provided with the tool
-checkpoints     = '/project/3015069.05/bids/code/deepMRI/BFRNet_data/checkpoints/BFRnet_L2_64PS_24BS_45Epo_NewHCmix.mat';
+checkpoints     = '/home/common/matlab/sepia/external/deepMRI/BFRNet_data/checkpoints/BFRnet_L2_64PS_24BS_45Epo_NewHCmix.mat';
 
diff --git a/addons/qsm/LPCNN/Wrapper_QSM_LPCNN.m b/addons/qsm/LPCNN/Wrapper_QSM_LPCNN.m
@@ -80,6 +80,8 @@
     mask_pad        = mask;
 end
 
+% 20231009: fix mismatch of B0dir between SEPIA and LPCNN
+b0dir = [b0dir(2), -b0dir(1), b0dir(3)];
 
 [C,~] = DipoleKernel(size(localField_pad),voxelSize,b0dir);
 

diff --git a/addons/qsm/LPCNN/setup_LPCNN_environment.m b/addons/qsm/LPCNN/setup_LPCNN_environment.m
@@ -3,9 +3,9 @@
 % dir_net             = fullfile(qsmnet_dir,'Checkpoints/');
 
 % Specify LPCNN_HOME corresponding to the code from Github
-LPCNN_HOME          = '/project/3015069.05/bids/code/LPCNN/';
+LPCNN_HOME          = '/home/common/matlab/sepia/external/LPCNN/LPCNN_v1.0';
 % Specify the Python environment that has QSMnet+ installed
-python_interpreter  = '/project/3015069.05/bids/code/LPCNN/lpcnn-env/bin/python';
+python_interpreter  = '/home/common/matlab/sepia/external/LPCNN/LPCNN_v1.0/lpcnn-env/bin/python';
 % Specify the directory that contains the training parameters
 checkpoint_fn       = fullfile(LPCNN_HOME,'checkpoints','lpcnn_test_Bmodel.pkl');
 % checkpoint_fn       = '/project/3015069.05/bids/code/LPCNN/checkpoints/lpcnn_test_Bmodel.pkl';

diff --git a/addons/qsm/QSMnet/setup_qsmnet_environment.m b/addons/qsm/QSMnet/setup_qsmnet_environment.m
@@ -1,8 +1,8 @@
 %% This file specifies the Python environment and Checkpoint of QSMnet+
 
 % Specify the directory of the QSMnet+ code from Github
-QSMnet_HOME         = '/project/3015069.05/bids/code/QSMnet/';
+QSMnet_HOME         = '/home/common/matlab/sepia/external/QSMnet/QSMnet-9ca283a';
 % Specify the Python environment that has QSMnet+ installed
-python_interpreter  = '/project/3015069.05/bids/code/QSMnet/qsmnet/bin/python';
+python_interpreter  = '/home/common/matlab/sepia/external/QSMnet/QSMnet-9ca283a/qsmnet/bin/python';
 % Specify the directory that contains the trained parameters
 dir_net             = fullfile(QSMnet_HOME,'Checkpoints/');
diff --git a/addons/qsm/xQSM/setup_xQSM_environment.m b/addons/qsm/xQSM/setup_xQSM_environment.m
@@ -1,7 +1,7 @@
 %% This file specifies the Checkpoint of xQSM
 
 % Specify the directory of the xQSM code from Github
-deepMRI_HOME   	= '/project/3015069.05/bids/code/deepMRI/';
+deepMRI_HOME   	= '/home/common/matlab/sepia/external/deepMRI/';
 % If you have your own trained network, specify the file that contains the trained parameters
 % otherwise, uses the one provided with the tool
 checkpoint_dir  = fullfile(deepMRI_HOME, 'xQSM_data','checkpoints');

diff --git a/sepia.m b/sepia.m
@@ -45,6 +45,7 @@
 % Date modified: 12 June 2021 (v1.0)
 % Date modified: 3 August 2022 (v1.1)
 % Date modified: 3 April 2023 (v1.2.2.4)
+% Date modified: 9 October 2023 (v1.2.2.5)
 %
 function sepia 
 

diff --git a/sepia_universal_variables.m b/sepia_universal_variables.m
@@ -14,7 +14,7 @@
 % DO NOT change the order of the entities, add a new one at the end instead
 %
 %% Version
-SEPIA_version = 'v1.2.2.4';
+SEPIA_version = 'v1.2.2.5';
 
 %% PATH
 SEPIA_HOME = fileparts(mfilename('fullpath'));