From 0b94beee2126c0c066be431e32c2a15539384959 Mon Sep 17 00:00:00 2001 From: Tengfei Xue <56477109+tengfeixue-victor@users.noreply.github.com> Date: Thu, 6 May 2021 13:22:13 +1000 Subject: [PATCH 1/7] Tensorflow2 update --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 9c8e11d..3521092 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,10 @@ This code implements a deep learning tractography segmentation method (DeepWMA) Deep white matter analysis (DeepWMA): fast and consistent tractography segmentation. Medical Image Analysis 65 (2020): 101761 +# Version update + +The tensorflow2 (2.3.0) version is in Tensorflow2 branch. + # Example See the following script for instructions: From e38a0917397d73d7786749223e164154d8b22168 Mon Sep 17 00:00:00 2001 From: Tengfei Xue <56477109+tengfeixue-victor@users.noreply.github.com> Date: Thu, 6 May 2021 13:22:42 +1000 Subject: [PATCH 2/7] Tensorflow2 update --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3521092..03a2a10 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ This code implements a deep learning tractography segmentation method (DeepWMA) # Version update -The tensorflow2 (2.3.0) version is in Tensorflow2 branch. +The Tensorflow2 (2.3.0) version is in Tensorflow2 branch. # Example From bfde2bcb41da2ebfa8c67feb261e6377d082d11a Mon Sep 17 00:00:00 2001 From: Tengfei Xue <56477109+tengfeixue-victor@users.noreply.github.com> Date: Thu, 6 May 2021 15:09:47 +1000 Subject: [PATCH 3/7] Tensorflow2 Update --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 03a2a10..248b10e 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # DeepWMA (Deep White Matter Analysis) +Please check **Tensorflow2 branch** for updates + This code implements a deep learning tractography segmentation method (DeepWMA) that allows fast and consistent white matter fiber tract identification, as described in the following paper: Fan Zhang, Suheyla Cetin Karayumak, Nico Hoffmann, Yogesh Rathi, Alexandra J. Golby, and Lauren J. O’Donnell. From b3b1870a010394917031a194caef53c2a5b14756 Mon Sep 17 00:00:00 2001 From: Tengfei Xue <56477109+tengfeixue-victor@users.noreply.github.com> Date: Mon, 21 Jun 2021 22:59:57 +1000 Subject: [PATCH 4/7] fix bilateral bugs --- src/tract_feat.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/tract_feat.py b/src/tract_feat.py index e8dd35d..50b0a9d 100644 --- a/src/tract_feat.py +++ b/src/tract_feat.py @@ -463,7 +463,7 @@ def bilateralize_feature_OLD(y_names, y_data, x_data, fliped_copy=False): # Replace y label of right structure to its corresponding left structure # Note: here we assume that right structure is next to the left structure - y_data_bilateral_ = y_data + y_data_bilateral_ = np.copy(y_data) for y_label in all_y_labels: if 'left' in y_names[y_label]: # print y_label, y_names[y_label], y_names[y_label+1] @@ -480,7 +480,7 @@ def bilateralize_feature_OLD(y_names, y_data, x_data, fliped_copy=False): y_names_bilateral = np.array(y_names_bilateral) # Make bilateral x data - x_data_reflected = x_data + x_data_reflected = np.copy(x_data) x_data_reflected[:,:,:,0] = -x_data_reflected[:,:,:,0] x_data_bilateral = np.concatenate((x_data, x_data_reflected), axis=2) @@ -649,7 +649,7 @@ def bilateralize_feature(y_data, y_names, y_validation=None, verbose=False): def bilateral_X_data(x_data, fliped_copy=False, y_data=None): - x_data_reflected = x_data + x_data_reflected = np.copy(x_data) x_data_reflected[:,:,:,0] = -x_data_reflected[:,:,:,0] if x_data_reflected.shape[-1] == 4: From dbd9482a2a0e3236d5d2f9c452e76c851dcfdbcb Mon Sep 17 00:00:00 2001 From: Tengfei Xue <56477109+tengfeixue-victor@users.noreply.github.com> Date: Mon, 21 Jun 2021 23:10:20 +1000 Subject: [PATCH 5/7] Update README.md --- README.md | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/README.md b/README.md index 248b10e..0669a24 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,11 @@ # DeepWMA (Deep White Matter Analysis) -Please check **Tensorflow2 branch** for updates - This code implements a deep learning tractography segmentation method (DeepWMA) that allows fast and consistent white matter fiber tract identification, as described in the following paper: Fan Zhang, Suheyla Cetin Karayumak, Nico Hoffmann, Yogesh Rathi, Alexandra J. Golby, and Lauren J. O’Donnell. Deep white matter analysis (DeepWMA): fast and consistent tractography segmentation. Medical Image Analysis 65 (2020): 101761 -# Version update - -The Tensorflow2 (2.3.0) version is in Tensorflow2 branch. - # Example See the following script for instructions: @@ -34,3 +28,4 @@ See the following script for instructions: Isaiah Norton, Walid Ibn Essayed, Fan Zhang, Sonia Pujol, Alex Yarmarkovich, Alexandra J. Golby, Gordon Kindlmann, Demian Wassermann, Raul San Jose Estepar, Yogesh Rathi, Steve Pieper, Ron Kikinis, Hans J. Johnson, Carl-Fredrik Westin and Lauren J. O'Donnell. SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research. Cancer Research 77(21), e101-e103, 2017. + From fc68ef8a85cea235a219649912935547b36a33ec Mon Sep 17 00:00:00 2001 From: Tengfei Xue <56477109+tengfeixue-victor@users.noreply.github.com> Date: Mon, 21 Jun 2021 23:16:36 +1000 Subject: [PATCH 6/7] Check tensorflow 2 version Please check TensorFlow 2 version in another branch --- README.md | 33 ++++++++++++++++++++++++--------- 1 file changed, 24 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 0669a24..512e084 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,26 @@ -# DeepWMA (Deep White Matter Analysis) +https://github.com/zhangfanmark/DeepWMA + +https://github.com/tengfeixue-victor/DeepWMA/tree/Tensorflow2 + +# DeepWMA (Deep White Matter Analysis) - Tensorflow2 This code implements a deep learning tractography segmentation method (DeepWMA) that allows fast and consistent white matter fiber tract identification, as described in the following paper: - Fan Zhang, Suheyla Cetin Karayumak, Nico Hoffmann, Yogesh Rathi, Alexandra J. Golby, and Lauren J. O’Donnell. + Fan Zhang, Suheyla Cetin Karayumak, Nico Hoffmann, Yogesh Rathi, Alexandra J. Golby, and Lauren J. O’Donnell. Deep white matter analysis (DeepWMA): fast and consistent tractography segmentation. Medical Image Analysis 65 (2020): 101761 +This version updates the code to the latest Tensorflow 2 environment. + +# Dependencies +Tensorflow == 2.3.0 + +Python == 3.6.13 + +Cuda == 10.1.243 + +Cudnn = 7.6.5 + # Example See the following script for instructions: @@ -14,18 +29,18 @@ See the following script for instructions: **Please cite the following papers:** - Fan Zhang, Suheyla Cetin Karayumak, Nico Hoffmann, Yogesh Rathi, Alexandra J. Golby, and Lauren J. O’Donnell. + Fan Zhang, Suheyla Cetin Karayumak, Nico Hoffmann, Yogesh Rathi, Alexandra J. Golby, and Lauren J. O’Donnell. Deep white matter analysis (DeepWMA): fast and consistent tractography segmentation. Medical Image Analysis 65 (2020): 101761 - Fam Zhang, Ye Wu, Isaiah Norton, Yogesh Rathi, Nikos Makris and Lauren J. O’Donnell. - An anatomically curated fiber clustering white matter atlas for consistent white matter tract parcellation across the lifespan. + Fam Zhang, Ye Wu, Isaiah Norton, Yogesh Rathi, Nikos Makris and Lauren J. O’Donnell. + An anatomically curated fiber clustering white matter atlas for consistent white matter tract parcellation across the lifespan. NeuroImage, 2018 (179): 429-447 - Fan Zhang, Thomas Noh, Parikshit Juvekar, Sarah F Frisken, Laura Rigolo, Isaiah Norton, Tina Kapur, Sonia Pujol, William Wells III, Alex Yarmarkovich, Gordon Kindlmann, Demian Wassermann, Raul San Jose Estepar, Yogesh Rathi, Ron Kikinis, Hans J Johnson, Carl-Fredrik Westin, Steve Pieper, Alexandra J Golby, Lauren J O'Donnell. - SlicerDMRI: Diffusion MRI and Tractography Research Software for Brain Cancer Surgery Planning and Visualization. + Fan Zhang, Thomas Noh, Parikshit Juvekar, Sarah F Frisken, Laura Rigolo, Isaiah Norton, Tina Kapur, Sonia Pujol, William Wells III, Alex Yarmarkovich, Gordon Kindlmann, Demian Wassermann, Raul San Jose Estepar, Yogesh Rathi, Ron Kikinis, Hans J Johnson, Carl-Fredrik Westin, Steve Pieper, Alexandra J Golby, Lauren J O'Donnell. + SlicerDMRI: Diffusion MRI and Tractography Research Software for Brain Cancer Surgery Planning and Visualization. JCO Clinical Cancer Informatics 4, e299-309, 2020. - - Isaiah Norton, Walid Ibn Essayed, Fan Zhang, Sonia Pujol, Alex Yarmarkovich, Alexandra J. Golby, Gordon Kindlmann, Demian Wassermann, Raul San Jose Estepar, Yogesh Rathi, Steve Pieper, Ron Kikinis, Hans J. Johnson, Carl-Fredrik Westin and Lauren J. O'Donnell. + + Isaiah Norton, Walid Ibn Essayed, Fan Zhang, Sonia Pujol, Alex Yarmarkovich, Alexandra J. Golby, Gordon Kindlmann, Demian Wassermann, Raul San Jose Estepar, Yogesh Rathi, Steve Pieper, Ron Kikinis, Hans J. Johnson, Carl-Fredrik Westin and Lauren J. O'Donnell. SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research. Cancer Research 77(21), e101-e103, 2017. From a224d4af6364c5b319d1f20b7f00568e81811f31 Mon Sep 17 00:00:00 2001 From: Tengfei Xue <56477109+tengfeixue-victor@users.noreply.github.com> Date: Mon, 21 Jun 2021 23:19:19 +1000 Subject: [PATCH 7/7] Update ReadMe This is the original ReadMe --- README.md | 33 +++++++++------------------------ 1 file changed, 9 insertions(+), 24 deletions(-) diff --git a/README.md b/README.md index 512e084..0669a24 100644 --- a/README.md +++ b/README.md @@ -1,26 +1,11 @@ -https://github.com/zhangfanmark/DeepWMA - -https://github.com/tengfeixue-victor/DeepWMA/tree/Tensorflow2 - -# DeepWMA (Deep White Matter Analysis) - Tensorflow2 +# DeepWMA (Deep White Matter Analysis) This code implements a deep learning tractography segmentation method (DeepWMA) that allows fast and consistent white matter fiber tract identification, as described in the following paper: - Fan Zhang, Suheyla Cetin Karayumak, Nico Hoffmann, Yogesh Rathi, Alexandra J. Golby, and Lauren J. O’Donnell. + Fan Zhang, Suheyla Cetin Karayumak, Nico Hoffmann, Yogesh Rathi, Alexandra J. Golby, and Lauren J. O’Donnell. Deep white matter analysis (DeepWMA): fast and consistent tractography segmentation. Medical Image Analysis 65 (2020): 101761 -This version updates the code to the latest Tensorflow 2 environment. - -# Dependencies -Tensorflow == 2.3.0 - -Python == 3.6.13 - -Cuda == 10.1.243 - -Cudnn = 7.6.5 - # Example See the following script for instructions: @@ -29,18 +14,18 @@ See the following script for instructions: **Please cite the following papers:** - Fan Zhang, Suheyla Cetin Karayumak, Nico Hoffmann, Yogesh Rathi, Alexandra J. Golby, and Lauren J. O’Donnell. + Fan Zhang, Suheyla Cetin Karayumak, Nico Hoffmann, Yogesh Rathi, Alexandra J. Golby, and Lauren J. O’Donnell. Deep white matter analysis (DeepWMA): fast and consistent tractography segmentation. Medical Image Analysis 65 (2020): 101761 - Fam Zhang, Ye Wu, Isaiah Norton, Yogesh Rathi, Nikos Makris and Lauren J. O’Donnell. - An anatomically curated fiber clustering white matter atlas for consistent white matter tract parcellation across the lifespan. + Fam Zhang, Ye Wu, Isaiah Norton, Yogesh Rathi, Nikos Makris and Lauren J. O’Donnell. + An anatomically curated fiber clustering white matter atlas for consistent white matter tract parcellation across the lifespan. NeuroImage, 2018 (179): 429-447 - Fan Zhang, Thomas Noh, Parikshit Juvekar, Sarah F Frisken, Laura Rigolo, Isaiah Norton, Tina Kapur, Sonia Pujol, William Wells III, Alex Yarmarkovich, Gordon Kindlmann, Demian Wassermann, Raul San Jose Estepar, Yogesh Rathi, Ron Kikinis, Hans J Johnson, Carl-Fredrik Westin, Steve Pieper, Alexandra J Golby, Lauren J O'Donnell. - SlicerDMRI: Diffusion MRI and Tractography Research Software for Brain Cancer Surgery Planning and Visualization. + Fan Zhang, Thomas Noh, Parikshit Juvekar, Sarah F Frisken, Laura Rigolo, Isaiah Norton, Tina Kapur, Sonia Pujol, William Wells III, Alex Yarmarkovich, Gordon Kindlmann, Demian Wassermann, Raul San Jose Estepar, Yogesh Rathi, Ron Kikinis, Hans J Johnson, Carl-Fredrik Westin, Steve Pieper, Alexandra J Golby, Lauren J O'Donnell. + SlicerDMRI: Diffusion MRI and Tractography Research Software for Brain Cancer Surgery Planning and Visualization. JCO Clinical Cancer Informatics 4, e299-309, 2020. - - Isaiah Norton, Walid Ibn Essayed, Fan Zhang, Sonia Pujol, Alex Yarmarkovich, Alexandra J. Golby, Gordon Kindlmann, Demian Wassermann, Raul San Jose Estepar, Yogesh Rathi, Steve Pieper, Ron Kikinis, Hans J. Johnson, Carl-Fredrik Westin and Lauren J. O'Donnell. + + Isaiah Norton, Walid Ibn Essayed, Fan Zhang, Sonia Pujol, Alex Yarmarkovich, Alexandra J. Golby, Gordon Kindlmann, Demian Wassermann, Raul San Jose Estepar, Yogesh Rathi, Steve Pieper, Ron Kikinis, Hans J. Johnson, Carl-Fredrik Westin and Lauren J. O'Donnell. SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research. Cancer Research 77(21), e101-e103, 2017.