Comments (5)
Thanks for pointing this out. It should be fixed now with the latest ANTsRNet repository. I had made some changes associated with our python analog (ANTsPyNet) and introduced a bug which I just fixed.
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I just ran it using the latest pull from ANTsRNet and it worked fine (see below).
Regarding your second question---readNIFTI
reads in the nifti image into a completely separate data object as an antsImage. There's no cross-compatibility.
$ Rscript Scripts/doWholeTumorSegmentation.R Data/Example/brats_tcia_pat222_2/T2.nii.gz Data/Example/brats_tcia_pat222_2/Flair.nii.gz Data/Example/brats_tcia_pat222_2/BrainExtractionMask.nii.gz output Data/Template/S_template3_resampled2.nii.gz
*** Successfully loaded .Rprofile ***
Loading required package: ANTsRCore
Attaching package: ‘ANTsRCore’
The following object is masked from ‘package:stats’:
var
The following objects are masked from ‘package:base’:
all, any, apply, max, min, prod, range, sum
Reading reorientation template Data/Template/S_template3_resampled2.nii.gz (elapsed time: 0.2036459 seconds)
Using TensorFlow backend.
WARNING:tensorflow:From /Users/ntustison/anaconda3/envs/r-tensorflow/lib/python3.6/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version.
Instructions for updating:
Colocations handled automatically by placer.
Loading weights file2019-07-30 06:45:10.653908: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
(elapsed time: 0.5730999 seconds)
Reading input. (elapsed time: 0.657131 seconds)
Normalizing to template and cropping to mask. (elapsed time: 1.60081 seconds)
Prediction and decoding (elapsed time: 26.28147 seconds)
Renormalize to native space (elapsed time: 0.7662148 seconds)
Writing output (elapsed time: 1.656777 seconds)
Total elapsed time: 30.96547 seconds
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Related Issues (20)
- External data? HOT 3
- note to self: need to fix
- Code error in the example for "createUnetModel2D" HOT 8
- 3D image dataset for a tutorial of image segmentation HOT 1
- Instructions for deepFlash and deepAtropos HOT 2
- CUDA and tensorflow-gpu on WSL2
- Remove unnecessary code? HOT 2
- Poor results in brainExtraction HOT 4
- Regarding 'desikanKillianyTourvilleLabeling' HOT 8
- Training with template base data augmentation HOT 5
- Cortical thickness: Error in atropos$probabilityImages[[4]] + atropos$probabilityimages[[5]] : HOT 2
- desikanKillianyTourvilleLabeling only produces few ROI stats HOT 1
- Huge memory usage after using desikanKillianyTourvilleLabeling() HOT 3
- Cortical thickness evaluation inconsistency!!! HOT 17
- Any possibility of refining DKT labels HOT 4
- Reference for DeepFlash HOT 1
- A 'tensorflow not found' error HOT 2
- Are ANTsRNet functions available for **training** and **testing** UNet models? HOT 5
- ANTsRNet/ANTsPyNet approaches to image registration HOT 2
- Installation Issue. HOT 3
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