Merge pull request #72 from arnaudbore/update_new_container

Update tractoflow - new container
scilus · Mar 24, 2023 · a4a7b2c · a4a7b2c
2 parents 72a8896 + 872facf
commit a4a7b2c
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/main.nf b/main.nf
@@ -1044,7 +1044,7 @@ process Normalize_DWI {
       scil_compute_dti_metrics.py dwi_dti.nii.gz bval_dti bvec_dti --mask $mask\
           --not_all --fa fa.nii.gz --force_b0_threshold
       mrthreshold fa.nii.gz ${sid}_fa_wm_mask.nii.gz -abs $params.fa_mask_threshold -nthreads 1
-      dwinormalise $dwi ${sid}_fa_wm_mask.nii.gz ${sid}__dwi_normalized.nii.gz\
+      dwinormalise individual $dwi ${sid}_fa_wm_mask.nii.gz ${sid}__dwi_normalized.nii.gz\
           -fslgrad $bvec $bval -nthreads 1
       """
     else
@@ -1061,7 +1061,7 @@ process Normalize_DWI {
         scil_compute_dti_metrics.py dwi_dti.nii.gz bval_dti bvec_dti --mask $mask\
             --not_all --fa fa.nii.gz --force_b0_threshold
         mrthreshold fa.nii.gz ${sid}_fa_wm_mask.nii.gz -abs $params.fa_mask_threshold -nthreads 1
-        dwinormalise $dwi ${sid}_fa_wm_mask.nii.gz ${sid}__dwi_normalized.nii.gz\
+        dwinormalise individual $dwi ${sid}_fa_wm_mask.nii.gz ${sid}__dwi_normalized.nii.gz\
             -fslgrad $bvec $bval -nthreads 1
       """
 

diff --git a/nextflow.config b/nextflow.config
@@ -45,7 +45,7 @@ params {
 
     //**Eddy**//
         run_eddy=true
-        eddy_cmd="eddy_openmp"
+        eddy_cmd="eddy_cpu"
         bet_topup_before_eddy_f=0.16
         use_slice_drop_correction=true