New function: sct_deepseg_lesion #1850
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
added 3 commits
June 13, 2018 10:38
|
@charleygros looks like Travis is failing due to install problem, do you want to fix it before i review? |
|
@charleygros Logs (sct_download_data): |
|
@jcohenadad : It should be fixed now. |
|
error with this commit fba8c86 probably because the model is not installed during SCT installation. It would need to be added. |
charleygros
force-pushed
the
cg_sct_deepseg_lesion
branch
from
fba8c86
to
3796362
Compare
|
(The models should now be available, except if I missed something else) |
|
@abtahizadeh could you please create a test for this function before we merge it? in the same vein as the other testing functions that already exist. No need for integrity testing at this point (but we can open an issue to address it in the future). Thanks! |
|
@jcohenadad okay, please allow me some time to understand the function. |
jcohenadad
approved these changes
Jul 11, 2018
jcohenadad
pushed a commit
that referenced
this pull request
Dec 18, 2019
* first implementation of sct_deepseg_lesion * add t2_ax contrast + threshold * models on OSF and neuropoly * add comma in sct_download_data * add deep_lesion_models to the list to download * installer: added download of deepseg_lesion models * TEST: added deepseg_lesion Former-commit-id: f4d917a
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
TODO
sct_deepseg_lesionGH labelDescription of the Change
AVAILABLE CONTRASTS:
{t2,t2s,t2_ax}-c t2_ax--> was train on ~200 3D T2-w volumes with anisotropic resolution, axial orientation.-c t2--> was train on 3D T2-w volumes with anisotropic resolution, both axial orientation and sagittal orientation.CENTERLINE DETECTION: 2 available ways to do it --> via the flag
-ctr-ctr svm--> OptiC initialized with SVM+HoG maps (former version, currently the one integrated in master). Avantages: faster, more robust to exotic / new contrasts.-ctr cnn--> OptiC initialized with CNN_1 maps. Avantages: more robust to compressed cord and/or sagittal images.DEALING WITH THE PRESENCE OF THE BRAIN:
-brain 0--> The algorithm will go through all the axial slices. Currently the version running in master. Note that this option is always set with -ctr svm.-brain 1--> If brain is detected (using the CNN1 previously mentioned), the segmentation algorithm will ignore axial slices above the brainstem. PROS: (i) speed up the segmentation (especially for sagittal images), (ii) Less false positive 'blobs' in the brain. CONS: The segmentation could sometimes stop below the brainstem.Steps and Constraints
/!\ Please re-install the toolbox: data folder