Fix deepseg threshold (again) (#2490)

* deepseg_sc/core: Fixed binarization after resampling * batch_processing.sh: Now outputtting T1 seg in QC * deepseg_sc/core: Updated optimal thresholds
spinalcordtoolbox · Oct 21, 2019 · d5d903a · d5d903a
1 parent d1cdb30
commit d5d903a
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diff --git a/batch_processing.sh b/batch_processing.sh
@@ -128,7 +128,7 @@ cd ..
 # ===========================================================================================
 cd t1
 # Segment spinal cord
-sct_deepseg_sc -i t1.nii.gz -c t1
+sct_deepseg_sc -i t1.nii.gz -c t1 -qc "$SCT_BP_QC_FOLDER"
 # Smooth spinal cord along superior-inferior axis
 sct_smooth_spinalcord -i t1.nii.gz -s t1_seg.nii.gz
 # Flatten cord in the right-left direction (to make nice figure)

diff --git a/spinalcordtoolbox/deepseg_sc/core.py b/spinalcordtoolbox/deepseg_sc/core.py
@@ -25,7 +25,7 @@
 # Thresholds to apply to binarize segmentations from the output of the 2D CNN. These thresholds were obtained by
 # minimizing the standard deviation of cross-sectional area across contrasts. For more details, see:
 # https:/sct-pipeline/deepseg-threshold
-THR_DEEPSEG = {'t1': 0.74353448, 't2': 0.34353448, 't2s': 0.89008621, 'dwi': 0.01422414}
+THR_DEEPSEG = {'t1': 0.15, 't2': 0.7, 't2s': 0.89, 'dwi': 0.01}
 
 logger = logging.getLogger(__name__)
 
@@ -548,7 +548,7 @@ def deep_segmentation_spinalcord(im_image, contrast_type, ctr_algo='cnn', ctr_fi
  # Binarize the resampled image (except for soft segmentation, defined by threshold_seg=-1)
  if threshold_seg >= 0:
  logger.info("Binarizing the resampled segmentation...")
- im_seg_r.data = im_seg_r.data.astype(np.uint8)
+ im_seg_r.data = (im_seg_r.data > 0.5).astype(np.uint8)
 
  # post processing step to z_regularized
  im_seg_r_postproc = post_processing_volume_wise(im_seg_r)