Speed up Jacobian det. computation

And compute the jacobian analysis on the warping field resulting from the registration (and not on the one transformed to the original space of the moving image).

Author: EvanBeal

eval_reg_with_jacobian.py

@@ -68,13 +68,10 @@
     dz = np.reshape((ddf[2:-2, 2:-2, :-4, :] - 8*ddf[2:-2, 2:-2, 1:-3, :] + 8*ddf[2:-2, 2:-2, 3:-1, :] - ddf[2:-2, 2:-2, 4:, :])/12.0, [num_voxel, num_channel])
     J = np.stack([dx, dy, dz], 2)
 
-    det = []
-    for voxel in range(num_voxel):
-        J[voxel, 0, 0] = J[voxel, 0, 0] + 1
-        J[voxel, 1, 1] = J[voxel, 1, 1] + 1
-        J[voxel, 2, 2] = J[voxel, 2, 2] + 1
-        n_array = J[voxel, :, :]
-        det.append(np.linalg.det(n_array))
+    J[:, 0, 0] = J[:, 0, 0] + 1
+    J[:, 1, 1] = J[:, 1, 1] + 1
+    J[:, 2, 2] = J[:, 2, 2] + 1
+    det = np.linalg.det(J)
 
     comparison = np.where(np.array(det) > 0, 0, np.array(det))  # all negatives values are there and positives become 0
     negative_dets = np.count_nonzero(comparison)

pipeline_bids_register_evaluate.sh

@@ -109,13 +109,13 @@ then
   file_fx="${SUBJECT_ID}_${SES}_${FX_NAME}_proc"
   file_mov="${SUBJECT_ID}_${SES}_${MOV_NAME}_proc"
   file_mov_reg="${SUBJECT_ID}_${SES}_${MOV_NAME}_proc_reg_to_${FX_NAME}"
-  file_warp="${SUBJECT_ID}_${SES}_${MOV_NAME}_warp_original_dim.nii.gz"
+  file_warp="${SUBJECT_ID}_${SES}_${MOV_NAME}_proc_field_to_${FX_NAME}.nii.gz"
   sub_id="${SUBJECT_ID}_${SES}"
 else
   file_fx="${SES}_${FX_NAME}_proc"
   file_mov="${SES}_${MOV_NAME}_proc"
   file_mov_reg="${SES}_${MOV_NAME}_proc_reg_to_${FX_NAME}"
-  file_warp="${SUBJECT_ID}_${SES}_${MOV_NAME}_warp_original_dim.nii.gz"
+  file_warp="${SES}_${MOV_NAME}_proc_field_to_${FX_NAME}.nii.gz"
   sub_id="${SES}"
 fi
 

pipeline_bids_register_evaluate_opt_affine.sh

@@ -114,13 +114,13 @@ then
   file_fx="${SUBJECT_ID}_${SES}_${FX_NAME}_proc"
   file_mov="${SUBJECT_ID}_${SES}_${MOV_NAME}_proc"
   file_mov_reg="${SUBJECT_ID}_${SES}_${MOV_NAME}_proc_reg_to_${FX_NAME}"
-  file_warp="${SUBJECT_ID}_${SES}_${MOV_NAME}_warp_original_dim.nii.gz"
+  file_warp="${SUBJECT_ID}_${SES}_${MOV_NAME}_proc_field_to_${FX_NAME}.nii.gz"
   sub_id="${SUBJECT_ID}_${SES}"
 else
   file_fx="${SES}_${FX_NAME}_proc"
   file_mov="${SES}_${MOV_NAME}_proc"
   file_mov_reg="${SES}_${MOV_NAME}_proc_reg_to_${FX_NAME}"
-  file_warp="${SUBJECT_ID}_${SES}_${MOV_NAME}_warp_original_dim.nii.gz"
+  file_warp="${SES}_${MOV_NAME}_proc_field_to_${FX_NAME}.nii.gz"
   sub_id="${SES}"
 fi
 

pipeline_bids_register_evaluate_two_steps.sh

@@ -118,13 +118,13 @@ then
   file_fx="${SUBJECT_ID}_${SES}_${FX_NAME}_proc"
   file_mov="${SUBJECT_ID}_${SES}_${MOV_NAME}_proc"
   file_mov_reg="${SUBJECT_ID}_${SES}_${MOV_NAME}_proc_reg_to_${FX_NAME}"
-  file_warp="${SUBJECT_ID}_${SES}_${MOV_NAME}_warp_original_dim.nii.gz"
+  file_warp="${SUBJECT_ID}_${SES}_${MOV_NAME}_proc_field_to_${FX_NAME}.nii.gz"
   sub_id="${SUBJECT_ID}_${SES}"
 else
   file_fx="${SES}_${FX_NAME}_proc"
   file_mov="${SES}_${MOV_NAME}_proc"
   file_mov_reg="${SES}_${MOV_NAME}_proc_reg_to_${FX_NAME}"
-  file_warp="${SES}_${MOV_NAME}_warp_original_dim.nii.gz"
+  file_warp="${SES}_${MOV_NAME}_proc_field_to_${FX_NAME}.nii.gz"
   sub_id="${SES}"
 fi