restore main.nf

scilus · Apr 19, 2021 · d53c3ad · d53c3ad
1 parent 433e922
commit d53c3ad
Showing 1 changed file with 20 additions and 17 deletions.
diff --git a/main.nf b/main.nf
@@ -359,8 +359,8 @@ process Bet_Prelim_DWI {
     scil_image_math.py convert ${sid}__b0_bet_mask.nii.gz ${sid}__b0_bet_mask.nii.gz --data_type uint8 -f
     maskfilter ${sid}__b0_bet_mask.nii.gz dilate ${sid}__b0_bet_mask_dilated.nii.gz\
         --npass $params.dilate_b0_mask_prelim_brain_extraction -nthreads 1
-    scil_image_math.py multiplication ${sid}__b0.nii.gz ${sid}__b0_bet_mask_dilated.nii.gz\
-      ${sid}__b0_bet.nii.gz -f
+    mrcalc ${sid}__b0.nii.gz ${sid}__b0_bet_mask_dilated.nii.gz\
+        -mult ${sid}__b0_bet.nii.gz -quiet -force -nthreads 1
     """
 }
 
@@ -385,7 +385,7 @@ process Denoise_DWI {
         export OMP_NUM_THREADS=1
         export OPENBLAS_NUM_THREADS=1
         dwidenoise $dwi dwi_denoised.nii.gz -extent $params.extent -nthreads $task.cpus
-        scil_image_math.py upper_threshold dwi_denoised.nii.gz 0 ${sid}__dwi_denoised.nii.gz -f
+        fslmaths dwi_denoised.nii.gz -thr 0 ${sid}__dwi_denoised.nii.gz
         """
     else
         """
@@ -478,7 +478,7 @@ process Eddy {
             --readout $readout --out_script --fix_seed\
             $slice_drop_flag
         sh eddy.sh
-        scil_image_math.py upper_threshold dwi_eddy_corrected.nii.gz 0 ${sid}__dwi_corrected.nii.gz -f
+        fslmaths dwi_eddy_corrected.nii.gz -thr 0 ${sid}__dwi_corrected.nii.gz
         mv dwi_eddy_corrected.eddy_rotated_bvecs ${sid}__dwi_eddy_corrected.bvec
         mv $bval ${sid}__bval_eddy
         """
@@ -541,7 +541,7 @@ process Eddy_Topup {
             --readout $readout --out_script --fix_seed\
             $slice_drop_flag
         sh eddy.sh
-        scil_image_math.py upper_threshold dwi_eddy_corrected.nii.gz 0 ${sid}__dwi_corrected.nii.gz -f
+        fslmaths dwi_eddy_corrected.nii.gz -thr 0 ${sid}__dwi_corrected.nii.gz
         mv dwi_eddy_corrected.eddy_rotated_bvecs ${sid}__dwi_eddy_corrected.bvec
         mv $bval ${sid}__bval_eddy
         """
@@ -612,8 +612,7 @@ process Bet_DWI {
     export OPENBLAS_NUM_THREADS=1
     bet $b0 ${sid}__b0_bet.nii.gz -m -R -f $params.bet_dwi_final_f
     scil_image_math.py convert ${sid}__b0_bet_mask.nii.gz ${sid}__b0_bet_mask.nii.gz --data_type uint8 -f
-    scil_image_math.py multiplication $dwi ${sid}__b0_bet_mask.nii.gz\
-      ${sid}__dwi_bet.nii.gz -f
+    mrcalc $dwi ${sid}__b0_bet_mask.nii.gz -mult ${sid}__dwi_bet.nii.gz -quiet -nthreads 1
     """
 }
 
@@ -759,8 +758,7 @@ process Bet_T1 {
     antsBrainExtraction.sh -d 3 -a $t1 -e $params.template_t1/t1_template.nii.gz\
         -o bet/ -m $params.template_t1/t1_brain_probability_map.nii.gz -u 0
     scil_image_math.py convert bet/BrainExtractionMask.nii.gz ${sid}__t1_bet_mask.nii.gz --data_type uint8
-    scil_image_math.py multiplication $t1 ${sid}__t1_bet_mask.nii.gz\
-      ${sid}__t1_bet.nii.gz -f
+    mrcalc $t1 ${sid}__t1_bet_mask.nii.gz -mult ${sid}__t1_bet.nii.gz -nthreads 1
     """
 }
 
@@ -835,18 +833,21 @@ process Resample_DWI {
     script:
     if (params.run_resample_dwi)
         """
+        export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+        export OMP_NUM_THREADS=1
+        export OPENBLAS_NUM_THREADS=1
         scil_resample_volume.py $dwi \
             dwi_resample.nii.gz \
             --resolution $params.dwi_resolution \
             --interp  $params.dwi_interpolation
-        scil_image_math.py upper_threshold dwi_resample.nii.gz 0 dwi_resample_clipped.nii.gz
+        fslmaths dwi_resample.nii.gz -thr 0 dwi_resample_clipped.nii.gz
         scil_resample_volume.py $mask \
             mask_resample.nii.gz \
             --ref dwi_resample.nii.gz \
             --enforce_dimensions \
             --interp nn
-        scil_image_math.py multiplication dwi_resample_clipped.nii.gz mask_resample.nii.gz\
-          ${sid}__dwi_resampled.nii.gz -f
+        mrcalc dwi_resample_clipped.nii.gz mask_resample.nii.gz\
+            -mult ${sid}__dwi_resampled.nii.gz -quiet -nthreads 1
         """
     else
         """
@@ -1261,7 +1262,7 @@ process PFT_Seeding_Mask {
         export OMP_NUM_THREADS=1
         export OPENBLAS_NUM_THREADS=1
         mrcalc $fa $params.pft_fa_seeding_mask_threshold -ge ${sid}__pft_seeding_mask.nii.gz\
-          -data_type uint8
+          -datatype uint8
         """
 }
 
@@ -1325,8 +1326,11 @@ process Local_Tracking_Mask {
         """
     else if (params.local_tracking_mask_type == "fa")
         """
-        scil_image_math.py lower_threshold_eq $fa $params.local_fa_tracking_mask_threshold ${sid}__local_tracking_mask.nii.gz\
-            --data_type uint8
+        export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+        export OMP_NUM_THREADS=1
+        export OPENBLAS_NUM_THREADS=1
+        mrcalc $fa $params.local_fa_tracking_mask_threshold -ge ${sid}__local_tracking_mask.nii.gz\
+          -datatype uint8
         """
 }
 
@@ -1356,8 +1360,7 @@ process Local_Seeding_Mask {
         export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
         export OMP_NUM_THREADS=1
         export OPENBLAS_NUM_THREADS=1
-        scil_image_math.py lower_threshold_eq $fa $params.local_fa_seeding_mask_threshold ${sid}__local_seeding_mask.nii.gz\
-            --data_type uint8
+        mrcalc $fa $params.local_fa_seeding_mask_threshold -ge ${sid}__local_seeding_mask.nii.gz -datatype uint8
         """
 }