An Unsupervised Learning Model for Deformable Medical Image Registration

[Paluck1Arora2]

Respected, Kindly provide the dataset of your code "https://github.com/balakg/voxelmorph/" which mentioned in train.py file base_data_dir = '/insert/your/path/here' train_vol_names = glob.glob(base_data_dir + 'train/vols/*.npz') random.shuffle(train_vol_names) We demonstrate our method on the task of brain MRI registration. We use a large-scale, multi-site, multi-study dataset of 7829 T1weighted brain MRI scans from eight publicly available datasets: ADNI [33], OASIS [29], ABIDE [31], ADHD200 [32], MCIC [19], PPMI [30], HABS [12], and Harvard GSP [20]. These lines mentioned in the dataset part of the paper. Can you please help me out. Please provide the dataset which was used in the code.

Thanks.

[adalca]

@Paluck1Arora2 because of the requirements of all those datasets, we cannot share the original datasets. However, we prepared some data that you can use at https://github.com/adalca/medical-datasets/blob/master/neurite-oasis.md.

Please note that the voxelmorph github as moved to http://voxelmorph.net/

[Paluck1Arora2]

Hi sir, Thank you so much for the reply. Sir, can you please help me how it works with this dataset. I wasn't able to download this dataset. It was very helpful for me.

On Mon, Jan 9, 2023 at 7:03 AM Adrian Dalca @.***> wrote:

@Paluck1Arora2 https://github.com/Paluck1Arora2 because of the requirements of all those datasets, we cannot share the original datasets. However, we prepared some data that you can use at https://github.com/adalca/medical-datasets/blob/master/neurite-oasis.md.

Please note that the voxelmorph github as moved to http://voxelmorph.net/

— Reply to this email directly, view it on GitHub https://github.com/balakg/voxelmorph/issues/7#issuecomment-1375001811, or unsubscribe https://github.com/notifications/unsubscribe-auth/A47BEQ3BA7PMQDR4W7A5AWDWRNTFZANCNFSM6AAAAAATKRSAQ4 . You are receiving this because you were mentioned.Message ID: @.***>

[adalca]

What error did you get when downloading the dataset? The links should work. E.g. for 2D: https://surfer.nmr.mgh.harvard.edu/ftp/data/neurite/data/neurite-oasis.2d.v1.0.tar

[Paluck1Arora2]

Hlo sir, I'm not able to download 3D images dataset. Can you please help me out. Also, I used different dataset at the place of base_data_dir. base_data_dir = '/insert/your/path/here' train_vol_names = glob.glob(base_data_dir + 'train/vols/*.npz')

i used " https://www.kaggle.com/code/yeonghyeon/convert-dicom-to-numpy-array-super-simple/data" this dataset. i faced this error [image: image.png]

Kindly help me to resolve this issue.

On Mon, Jan 9, 2023 at 7:39 PM Adrian Dalca @.***> wrote:

What error did you get when downloading the dataset? The links should work. E.g. for 2D: https://surfer.nmr.mgh.harvard.edu/ftp/data/neurite/data/neurite-oasis.2d.v1.0.tar

— Reply to this email directly, view it on GitHub https://github.com/balakg/voxelmorph/issues/7#issuecomment-1375678907, or unsubscribe https://github.com/notifications/unsubscribe-auth/A47BEQ7VHNGCAJZN3URJA6LWRQL2VANCNFSM6AAAAAATKRSAQ4 . You are receiving this because you were mentioned.Message ID: @.***>

[adalca]

I'm not able to download 3D images dataset. Can you please help me out.

Can you please tell me what the problem/error is?

i faced this error [image: image.png]

This is an interesting dataset, but not one we are familiar with. I also don't see the image.

[Paluck1Arora2]

This is the link of file https://colab.research.google.com/drive/1HY3Sida46lRbbEQlZMSf0GsAn5FMBJvG?usp=sharing This is the link to the dataset. https://drive.google.com/drive/folders/1dnjYoVolFc2NYYiKpnxsPXXQdOpeOXMo?usp=sharing Following this dataset https://www.kaggle.com/code/yeonghyeon/convert-dicom-to-numpy-array-super-simple/data I have changed the path --train.py Can you please resolve this issue.

On Sun, Jan 15, 2023 at 8:43 PM Adrian Dalca @.***> wrote:

I'm not able to download 3D images dataset. Can you please help me out.

Can you please tell me what the problem/error is?

i faced this error [image: image.png] This is an interesting dataset, but not one we are familiar with. I also don't see the image.

— Reply to this email directly, view it on GitHub https://github.com/balakg/voxelmorph/issues/7#issuecomment-1383176922, or unsubscribe https://github.com/notifications/unsubscribe-auth/A47BEQ4ZGB4SK7B4XBWVOSTWSQHZDANCNFSM6AAAAAATKRSAQ4 . You are receiving this because you were mentioned.Message ID: @.***>

[adalca]

Sorry but you are not answering the question about the dataset.

What error did you get when downloading the dataset? The links should work. E.g. for 2D: https://surfer.nmr.mgh.harvard.edu/ftp/data/neurite/data/neurite-oasis.2d.v1.0.tar

As mentioned, this current repository is quite old, please use the code at voxelmorph.net

We also have an extensive tutorial on how to use voxelmorph at http://tutorial.voxelmorph.net/

[Paluck1Arora2]

Hi, I studied http://tutorial.voxelmorph.net/ this tutorial. In which one medical dataset is discussed which also has one static image. I checked this code https://github.com/voxelmorph/voxelmorph but facing the problem in the same. This is not executing.

On Sun, Jan 15, 2023 at 10:04 PM Adrian Dalca @.***> wrote:

Sorry but you are not answering the question about the dataset.

What error did you get when downloading the dataset? The links should work. E.g. for 2D: https://surfer.nmr.mgh.harvard.edu/ftp/data/neurite/data/neurite-oasis.2d.v1.0.tar

As mentioned, this current repository is quite old, please use the code at voxelmorph.net https://github.com/voxelmorph/voxelmorph

We also have an extensive tutorial on how to use voxelmorph at http://tutorial.voxelmorph.net/

— Reply to this email directly, view it on GitHub https://github.com/balakg/voxelmorph/issues/7#issuecomment-1383194465, or unsubscribe https://github.com/notifications/unsubscribe-auth/A47BEQ4WUFJ7BE6CE3LX4JLWSQRIHANCNFSM6AAAAAATKRSAQ4 . You are receiving this because you were mentioned.Message ID: @.***>

[Paluck1Arora2]

https://colab.research.google.com/drive/1FG78lk9P89mvtU62U_PRkhiKXwSGXDG4?usp=sharing I have checked https://github.com/voxelmorph/voxelmorph this code but facing issue. Can you please fix thi sissue

On Sun, Jan 15, 2023 at 10:18 PM PHD Arora @.***> wrote:

Hi, I studied http://tutorial.voxelmorph.net/ this tutorial. In which one medical dataset is discussed which also has one static image. I checked this code https://github.com/voxelmorph/voxelmorph but facing the problem in the same. This is not executing.

On Sun, Jan 15, 2023 at 10:04 PM Adrian Dalca @.***> wrote:

Sorry but you are not answering the question about the dataset.

What error did you get when downloading the dataset? The links should work. E.g. for 2D: https://surfer.nmr.mgh.harvard.edu/ftp/data/neurite/data/neurite-oasis.2d.v1.0.tar

As mentioned, this current repository is quite old, please use the code at voxelmorph.net https://github.com/voxelmorph/voxelmorph

We also have an extensive tutorial on how to use voxelmorph at http://tutorial.voxelmorph.net/

— Reply to this email directly, view it on GitHub https://github.com/balakg/voxelmorph/issues/7#issuecomment-1383194465, or unsubscribe https://github.com/notifications/unsubscribe-auth/A47BEQ4WUFJ7BE6CE3LX4JLWSQRIHANCNFSM6AAAAAATKRSAQ4 . You are receiving this because you were mentioned.Message ID: @.***>

[Paluck1Arora2]

Hi, Can you please resolve this issue.

On Sun, Jan 15, 2023 at 10:26 PM PHD Arora @.***> wrote:

https://colab.research.google.com/drive/1FG78lk9P89mvtU62U_PRkhiKXwSGXDG4?usp=sharing I have checked https://github.com/voxelmorph/voxelmorph this code but facing issue. Can you please fix thi sissue

On Sun, Jan 15, 2023 at 10:18 PM PHD Arora @.***> wrote:

Hi, I studied http://tutorial.voxelmorph.net/ this tutorial. In which one medical dataset is discussed which also has one static image. I checked this code https://github.com/voxelmorph/voxelmorph but facing the problem in the same. This is not executing.

On Sun, Jan 15, 2023 at 10:04 PM Adrian Dalca @.***> wrote:

Sorry but you are not answering the question about the dataset.

What error did you get when downloading the dataset? The links should work. E.g. for 2D: https://surfer.nmr.mgh.harvard.edu/ftp/data/neurite/data/neurite-oasis.2d.v1.0.tar

As mentioned, this current repository is quite old, please use the code at voxelmorph.net https://github.com/voxelmorph/voxelmorph

We also have an extensive tutorial on how to use voxelmorph at http://tutorial.voxelmorph.net/

— Reply to this email directly, view it on GitHub https://github.com/balakg/voxelmorph/issues/7#issuecomment-1383194465, or unsubscribe https://github.com/notifications/unsubscribe-auth/A47BEQ4WUFJ7BE6CE3LX4JLWSQRIHANCNFSM6AAAAAATKRSAQ4 . You are receiving this because you were mentioned.Message ID: @.***>

[Paluck1Arora2]

Hi, [image: image.png] [image: image.png] I'm getting these types of errors. Can you please resolve this issue

On Mon, Jan 16, 2023 at 5:08 PM PHD Arora @.***> wrote:

Hi, Can you please resolve this issue.

On Sun, Jan 15, 2023 at 10:26 PM PHD Arora @.***> wrote:

https://colab.research.google.com/drive/1FG78lk9P89mvtU62U_PRkhiKXwSGXDG4?usp=sharing I have checked https://github.com/voxelmorph/voxelmorph this code but facing issue. Can you please fix thi sissue

On Sun, Jan 15, 2023 at 10:18 PM PHD Arora @.***> wrote:

Hi, I studied http://tutorial.voxelmorph.net/ this tutorial. In which one medical dataset is discussed which also has one static image. I checked this code https://github.com/voxelmorph/voxelmorph but facing the problem in the same. This is not executing.

On Sun, Jan 15, 2023 at 10:04 PM Adrian Dalca @.***> wrote:

Sorry but you are not answering the question about the dataset.

What error did you get when downloading the dataset? The links should work. E.g. for 2D: https://surfer.nmr.mgh.harvard.edu/ftp/data/neurite/data/neurite-oasis.2d.v1.0.tar

As mentioned, this current repository is quite old, please use the code at voxelmorph.net https://github.com/voxelmorph/voxelmorph

We also have an extensive tutorial on how to use voxelmorph at http://tutorial.voxelmorph.net/

— Reply to this email directly, view it on GitHub https://github.com/balakg/voxelmorph/issues/7#issuecomment-1383194465, or unsubscribe https://github.com/notifications/unsubscribe-auth/A47BEQ4WUFJ7BE6CE3LX4JLWSQRIHANCNFSM6AAAAAATKRSAQ4 . You are receiving this because you were mentioned.Message ID: @.***>

[adalca]

I cannot see these images, it simply says [image: image.png]. When you send images, please try to make sure they show up on the github page.

I quickly coded up a colab that shows how to train on the OASIS data that we preprocessed and provide freely: https://colab.research.google.com/drive/1ZefmWXBupRNsnIbBbGquhVDsk-7R7L1S?usp=sharing

[Paluck1Arora2]

Hi, please check this colab notebook " https://colab.research.google.com/drive/1FG78lk9P89mvtU62U_PRkhiKXwSGXDG4?usp=sharing " I'm facing these issues.Can you please resolve it. Thank you so much for the reply.

On Tue, Jan 17, 2023 at 1:22 AM Adrian Dalca @.***> wrote:

I cannot see these images, it simply says [image: image.png]. When you send images, please try to make sure they show up on the github page.

I quickly coded up a colab that shows how to train on the OASIS data that we preprocessed and provide freely: https://colab.research.google.com/drive/1ZefmWXBupRNsnIbBbGquhVDsk-7R7L1S?usp=sharing

— Reply to this email directly, view it on GitHub https://github.com/balakg/voxelmorph/issues/7#issuecomment-1384489070, or unsubscribe https://github.com/notifications/unsubscribe-auth/A47BEQ2FWU576FAXLX4CBFTWSWRHBANCNFSM6AAAAAATKRSAQ4 . You are receiving this because you were mentioned.Message ID: @.***>

[adalca]

Sorry, we don't have the bandwidth to closely debug user's scripts. I provided a colab above that works from scratch -- downloads recent voxelmorph from the git, downloads OASIS, and starts training with train.py. I recommend you remove all your files from scratch and try again using this tutorial. It shold work and give you a starting point.

[Paluck1Arora2]

Thank you so much sir. I got error in your file.

On Tue, Jan 17, 2023 at 6:18 PM Adrian Dalca @.***> wrote:

Sorry, we don't have the bandwidth to closely debug user's scripts. I provided a colab above that works from scratch -- downloads recent voxelmorph from the git, downloads OASIS, and starts training with train.py. I recommend you remove all your files from scratch and try again using this tutorial. It shold work and give you a starting point.

— Reply to this email directly, view it on GitHub https://github.com/balakg/voxelmorph/issues/7#issuecomment-1385375561, or unsubscribe https://github.com/notifications/unsubscribe-auth/A47BEQ7CP76TIFXNN6JKB2TWS2IKLANCNFSM6AAAAAATKRSAQ4 . You are receiving this because you were mentioned.Message ID: @.***>

[Paluck1Arora2]

Hlo sir, Can you please tell me how to compute the average dice score in a voxel morph tutorial in 2d images. https://colab.research.google.com/drive/1WiqyF7dCdnNBIANEY80Pxw_mVz4fyV-S?usp=sharing#scrollTo=1axrla6VPXPf

On Tue, Jan 17, 2023 at 11:17 PM PHD Arora @.***> wrote:

Thank you so much sir. I got error in your file.

On Tue, Jan 17, 2023 at 6:18 PM Adrian Dalca @.***> wrote:

Sorry, we don't have the bandwidth to closely debug user's scripts. I provided a colab above that works from scratch -- downloads recent voxelmorph from the git, downloads OASIS, and starts training with train.py. I recommend you remove all your files from scratch and try again using this tutorial. It shold work and give you a starting point.

— Reply to this email directly, view it on GitHub https://github.com/balakg/voxelmorph/issues/7#issuecomment-1385375561, or unsubscribe https://github.com/notifications/unsubscribe-auth/A47BEQ7CP76TIFXNN6JKB2TWS2IKLANCNFSM6AAAAAATKRSAQ4 . You are receiving this because you were mentioned.Message ID: @.***>

[Paluck1Arora2]

Hi sir, Can you please inform me how to compute gpu time and different values of lambda in 3d voxelmorph. Please resolve these issues . https://www.kaggle.com/code/kmader/voxelmorph-demo/notebook

On Mon, Jan 9, 2023 at 7:03 AM Adrian Dalca @.***> wrote:

@Paluck1Arora2 https://github.com/Paluck1Arora2 because of the requirements of all those datasets, we cannot share the original datasets. However, we prepared some data that you can use at https://github.com/adalca/medical-datasets/blob/master/neurite-oasis.md.

Please note that the voxelmorph github as moved to http://voxelmorph.net/

— Reply to this email directly, view it on GitHub https://github.com/balakg/voxelmorph/issues/7#issuecomment-1375001811, or unsubscribe https://github.com/notifications/unsubscribe-auth/A47BEQ3BA7PMQDR4W7A5AWDWRNTFZANCNFSM6AAAAAATKRSAQ4 . You are receiving this because you were mentioned.Message ID: @.***>

[Paluck1Arora2]

Sir, you have written paper and many codes in this area. Kindly help me to resolve the issues!

On Tue, Jan 17, 2023 at 1:22 AM Adrian Dalca @.***> wrote:

I cannot see these images, it simply says [image: image.png]. When you send images, please try to make sure they show up on the github page.

I quickly coded up a colab that shows how to train on the OASIS data that we preprocessed and provide freely: https://colab.research.google.com/drive/1ZefmWXBupRNsnIbBbGquhVDsk-7R7L1S?usp=sharing

— Reply to this email directly, view it on GitHub https://github.com/balakg/voxelmorph/issues/7#issuecomment-1384489070, or unsubscribe https://github.com/notifications/unsubscribe-auth/A47BEQ2FWU576FAXLX4CBFTWSWRHBANCNFSM6AAAAAATKRSAQ4 . You are receiving this because you were mentioned.Message ID: @.***>

[adalca]

As mentioned, this is not the right github repository. Please refer to voxelmorph