osandvold302 / trabecular_bone_unet Goto Github PK
View Code? Open in Web Editor NEWRajapakse/Jones project for reconstructing artificially undersampled kspace MRI scans of hips. Based on work completed by bcjones to reconstruct 2D images.
Rajapakse/Jones project for reconstructing artificially undersampled kspace MRI scans of hips. Based on work completed by bcjones to reconstruct 2D images.
undersampled_sample = np.multiply(np.reshape(full_kspace[counter, 0, :, :, :], (num_slices, img_height, img_width)), mask_2d)
undersampled_kspace[counter, 0, :, :, :] = np.reshape(undersampled_sample, (img_height, img_width, num_slices))
@brandonclintonjones when undersampling the 3d volume kspace, does this reshaping seem appropriate?
to recall: full_kspace
would be (512,512,60)
and mask_2d.shape = (512,512)
. The undersampled_kspace
has resulting size (num_scans, 1, 512, 512, 60)
To do some quick prototyping/testing I've been creating the conda environment with the environment.yml
file on the add-3d-option
branch and setting max_iter =1 for generating the pdf.
@brandonclintonjones I'm not going to assign you to this issue, because then I think you'll get updates every time a push occurs? Or if I'm just using this space to think out loud. So I'll try to ping you if there's something specific I'm asking.
Here's a few questions right off the bat on 3D implementation:
Assumptions about generated undersampled kspace
Because we'll be needing 2 different kspace undersampled "images" for 3D, what can we assume about the optimization for finding the least interference for the resulting volume?
Does the pdf need to change in both directions or just the depth direction?
Fails to build cnn on lsni2
2020-08-02 16:23:13.432065: W tensorflow/core/framework/op_kernel.cc:1273] OP_REQUIRES failed at conv_ops_3d.cc:161 : Resource exhausted: OOM when allocating tensor with shape[25,32,512,512,64] and type float on /job:localhost/replica:0/task:0/device:GPU:0 by allocator GPU_0_bfc
But I'm pretty sure it's using the new GPU:
Found device 0 with properties:
name: Tesla V100-PCIE-32GB major: 7 minor: 0 memoryClockRate(GHz): 1.38
pciBusID: 0000:d8:00.0
2020-08-02 16:27:00.998709: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1115] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 30511 MB memory) -> physical GPU (device: 0, name: Tesla V100-PCIE-32GB, pci bus id: 0000:d8:00.0, compute capability: 7.0)
I decreased my batch size to 3. Only using the 9 layers (from this post it seems like that's well below concern).
Attached full output
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.