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--- |
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license: afl-3.0 |
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tags: |
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- medical |
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size_categories: |
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- 100M<n<1B |
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--- |
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# Dataset for AVS-Net Pre-training |
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The dataset utilized in the pre-training of the AVS-Net: Attention-based Variable Splitting Network for P-MRI Acceleration model, developed by Y Zhang, J Li, Z Wang, J Duan, and J Li, incorporates data from five distinct protocol sequences. These are: |
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- (coronal_pd)Coronal Spin Density-weighted without Fat Suppression |
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- (coronal_pd_fs)Coronal Spin Density-weighted with Fat Suppression |
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- (sagittal_pd)Sagittal Spin Density-weighted |
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- (sagittal_t2)Sagittal T2-weighted with Fat Suppression |
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- (axial_t2)Axial T2-weighted with Fat Suppression |
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The dataset is structured on a slice-by-slice basis, with each slice containing 20 cases. Each case is comprised of two files: rawdata*.mat and espirit*.mat. The dataset's structure can be outlined as follows: |
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## Dataset architecture: |
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- name: /rds/projects/d/duanj-ai-in-medical-imaging/knee_fast_mri |
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- Protocol: [coronal_pd, coronal_pd_fs, sagittal_pd, sagittal_t2, axial_t2] |
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Approximately 40 slices per protocol, each slice containing 15 channels, with a height and width (HW) of (640, 368) |
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``` |
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knee_nyu |
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- axial_t2 coronal_pd(X) coronal_pd_fs sagittal_pd sagittal_t2 |
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- [1, 2, 3, 4, 5, 6, 7, 8, 9, 10], [11, 12, 13, 14, 15, 16, 17, 18, 19, 20] masks |
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- [train] [val] |
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- espirit*.mat(1-40), rawdata*.mat(1-40) *_masks.mat |
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``` |
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In this structure, each protocol has approximately 40 slices, each consisting of 15 channels. The dimensions of the data are 640x368 (height x width). For each protocol, the slices are further divided into two groups: the training set ([train]) and the validation set ([val]). The training set includes the espirit*.mat and rawdata*.mat files for each slice, while the validation set contains *_masks.mat files. |
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## Dataset Usage |
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> For a standalone knee dataset download, use `git lfs`(<https://git-lfs.com/>) to download from the `huggingface` datasets(<https://huggingface.co/datasets/AVS-Net/knee_fast_mri>): |
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```bash |
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# Make sure you have git-lfs installed (https://git-lfs.com) |
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git lfs install |
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git clone -j8 [email protected]:datasets/AVS-Net/knee_fast_mri |
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``` |
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## Known Issues and Resolutions |
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- 1. Network Connection Issue |
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For enhanced network connection quality, it is recommended to employ the `ssh` protocol instead of `https`. |
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```bash |
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# Rather than utilizing `https://huggingface.co/datasets/AVS-Net/knee_fast_mri` |
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# Clone the repository using `[email protected]:datasets/AVS-Net/knee_fast_mri` |
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# As an example: |
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git clone -j8 [email protected]:datasets/AVS-Net/knee_fast_mri |
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``` |
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- 2. Interruptions During Download |
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Certain error messages may appear during the download process due to interruptions. These errors can include: |
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``` |
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error: ... : cannot add to the index - missing --add option? |
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batch response: Post ... : read: connection reset by peer |
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error: failed to fetch some objects from 'https://hf.co/datasets/AVS-Net/knee_fast_mri.git/info/lfs' |
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``` |
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Following the instructions below allows for the handling of these interruptions. |
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```bash |
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# Navigate (`cd`) to the directory containing the `lfs` folder |
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# Intead of using `git pull`, |
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# Use `git lfs pull` to resume the download progress for `lfs` projects |
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git lfs pull |
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``` |
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Please note that this process will resume the download from where it was interrupted, thereby ensuring the integrity of your downloaded data. |
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