From 8f9c22746834714602c907e7813c5e8f864a6386 Mon Sep 17 00:00:00 2001 From: Arnaud Bore Date: Sun, 18 Apr 2021 22:51:14 -0400 Subject: [PATCH 1/3] remove all fslmath and mrcalc --- main.nf | 37 ++++++++++++++++++------------------- 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/main.nf b/main.nf index d2136a0..513b0e3 100755 --- 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 - mrcalc ${sid}__b0.nii.gz ${sid}__b0_bet_mask_dilated.nii.gz\ - -mult ${sid}__b0_bet.nii.gz -quiet -force -nthreads 1 + scil_image_math.py multiplication ${sid}__b0.nii.gz ${sid}__b0_bet_mask_dilated.nii.gz\ + ${sid}__b0_bet.nii.gz -f """ } @@ -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 - fslmaths dwi_denoised.nii.gz -thr 0 ${sid}__dwi_denoised.nii.gz + scil_image_math.py upper_threshold dwi_denoised.nii.gz 0 ${sid}__dwi_denoised.nii.gz -f """ else """ @@ -478,7 +478,7 @@ process Eddy { --readout $readout --out_script --fix_seed\ $slice_drop_flag sh eddy.sh - fslmaths dwi_eddy_corrected.nii.gz -thr 0 ${sid}__dwi_corrected.nii.gz + scil_image_math.py upper_threshold dwi_eddy_corrected.nii.gz 0 ${sid}__dwi_corrected.nii.gz -f 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 - fslmaths dwi_eddy_corrected.nii.gz -thr 0 ${sid}__dwi_corrected.nii.gz + scil_image_math.py upper_threshold dwi_eddy_corrected.nii.gz 0 ${sid}__dwi_corrected.nii.gz -f mv dwi_eddy_corrected.eddy_rotated_bvecs ${sid}__dwi_eddy_corrected.bvec mv $bval ${sid}__bval_eddy """ @@ -612,7 +612,8 @@ 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 - mrcalc $dwi ${sid}__b0_bet_mask.nii.gz -mult ${sid}__dwi_bet.nii.gz -quiet -nthreads 1 + scil_image_math.py multiplication $dwi ${sid}__b0_bet_mask.nii.gz\ + ${sid}__dwi_bet.nii.gz -f """ } @@ -758,7 +759,8 @@ 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 - mrcalc $t1 ${sid}__t1_bet_mask.nii.gz -mult ${sid}__t1_bet.nii.gz -nthreads 1 + scil_image_math.py multiplication $t1 ${sid}__t1_bet_mask.nii.gz\ + ${sid}__t1_bet.nii.gz -f """ } @@ -833,21 +835,18 @@ 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 - fslmaths dwi_resample.nii.gz -thr 0 dwi_resample_clipped.nii.gz + scil_image_math.py upper_threshold dwi_resample.nii.gz 0 dwi_resample_clipped.nii.gz scil_resample_volume.py $mask \ mask_resample.nii.gz \ --ref dwi_resample.nii.gz \ --enforce_dimensions \ --interp nn - mrcalc dwi_resample_clipped.nii.gz mask_resample.nii.gz\ - -mult ${sid}__dwi_resampled.nii.gz -quiet -nthreads 1 + scil_image_math.py multiplication dwi_resample_clipped.nii.gz mask_resample.nii.gz\ + ${sid}__dwi_resampled.nii.gz -f """ else """ @@ -1261,7 +1260,8 @@ process PFT_Seeding_Mask { export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1 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 + scil_image_math.py lower_threshold_eq $fa $params.pft_fa_seeding_mask_threshold ${sid}__pft_seeding_mask.nii.gz\ + --data_type uint8 """ } @@ -1325,10 +1325,8 @@ process Local_Tracking_Mask { """ else if (params.local_tracking_mask_type == "fa") """ - 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 + scil_image_math.py lower_threshold_eq $fa $params.local_fa_tracking_mask_threshold ${sid}__local_tracking_mask.nii.gz\ + --data_type uint8 """ } @@ -1358,7 +1356,8 @@ process Local_Seeding_Mask { export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1 export OMP_NUM_THREADS=1 export OPENBLAS_NUM_THREADS=1 - mrcalc $fa $params.local_fa_seeding_mask_threshold -ge ${sid}__local_seeding_mask.nii.gz -datatype uint8 + scil_image_math.py lower_threshold_eq $fa $params.local_fa_seeding_mask_threshold ${sid}__local_seeding_mask.nii.gz\ + --data_type uint8 """ } From 21275dae0335312cfc1e8bcb0ff3dc8a26a98454 Mon Sep 17 00:00:00 2001 From: Arnaud Bore Date: Sun, 18 Apr 2021 22:54:25 -0400 Subject: [PATCH 2/3] fix --- main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/main.nf b/main.nf index d2136a0..2dfbe4b 100755 --- a/main.nf +++ b/main.nf @@ -1261,7 +1261,8 @@ process PFT_Seeding_Mask { export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1 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 + mrcalc $fa $params.pft_fa_seeding_mask_threshold -ge ${sid}__pft_seeding_mask.nii.gz\ + -data_type uint8 """ } From d53c3addeb247de3d201e472ac6c57ecd74480d1 Mon Sep 17 00:00:00 2001 From: Arnaud Bore Date: Mon, 19 Apr 2021 15:18:07 -0400 Subject: [PATCH 3/3] restore main.nf --- main.nf | 37 ++++++++++++++++++++----------------- 1 file changed, 20 insertions(+), 17 deletions(-) diff --git a/main.nf b/main.nf index 649c493..18c18e3 100755 --- 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 """ }