added lesion mask support

run_template_construction.py

@@ -53,7 +53,7 @@ def writeConfig(step,mod,fpath):
             '; Whole-head T1 \n' \
             'use_implicit_mask       = 0 \n' \
             'use_mask_ref_scalar     = 1 1 \n' \
-            'use_mask_mov_scalar     = 0 0 \n' \
+            'use_mask_mov_scalar     = 1 1 \n' \
             'fwhm_ref_scalar         = 8.0 8.0 \n' \
             'fwhm_mov_scalar         = 8.0 8.0 \n' \
             'lambda_scalar           = 1 1 \n' \
@@ -93,7 +93,7 @@ def writeConfig(step,mod,fpath):
             '; Whole-head T1 \n' \
             'use_implicit_mask       = 0 \n' \
             'use_mask_ref_scalar     = 1 1 1 \n' \
-            'use_mask_mov_scalar     = 0 0 0 \n' \
+            'use_mask_mov_scalar     = 1 1 1 \n' \
             'fwhm_ref_scalar         = 8.0 8.0 4.0 \n' \
             'fwhm_mov_scalar         = 8.0 8.0 4.0 \n' \
             'lambda_scalar           = 1 1 1 \n' \
@@ -133,7 +133,7 @@ def writeConfig(step,mod,fpath):
             '; Whole-head T1 \n' \
             'use_implicit_mask       = 0 \n' \
             'use_mask_ref_scalar     = 1 1 1 1 \n' \
-            'use_mask_mov_scalar     = 0 0 0 0 \n' \
+            'use_mask_mov_scalar     = 1 1 1 1 \n' \
             'fwhm_ref_scalar         = 8.0 8.0 4.0 2.0 \n' \
             'fwhm_mov_scalar         = 8.0 8.0 4.0 2.0 \n' \
             'lambda_scalar           = 1 1 1 1 \n' \
@@ -173,7 +173,7 @@ def writeConfig(step,mod,fpath):
             '; Whole-head T1 \n' \
             'use_implicit_mask       = 0 \n' \
             'use_mask_ref_scalar     = 1 1 1 1 1 \n' \
-            'use_mask_mov_scalar     = 0 0 0 0 0 \n' \
+            'use_mask_mov_scalar     = 1 1 1 1 1 \n' \
             'fwhm_ref_scalar         = 8.0 8.0 4.0 2.0 1.0 \n' \
             'fwhm_mov_scalar         = 8.0 8.0 4.0 2.0 1.0 \n' \
             'lambda_scalar           = 1 1 1 1 1 \n' \
@@ -213,7 +213,7 @@ def writeConfig(step,mod,fpath):
             '; Whole-head T1 \n' \
             'use_implicit_mask       = 0 \n' \
             'use_mask_ref_scalar     = 1 1 1 1 1 1 \n' \
-            'use_mask_mov_scalar     = 0 0 0 0 0 0 \n' \
+            'use_mask_mov_scalar     = 1 1 1 1 1 1 \n' \
             'fwhm_ref_scalar         = 8.0 8.0 4.0 2.0 1.0 0.5 \n' \
             'fwhm_mov_scalar         = 8.0 8.0 4.0 2.0 1.0 0.5 \n' \
             'lambda_scalar           = 1 1 1 1 1 1 \n' \
@@ -253,7 +253,7 @@ def writeConfig(step,mod,fpath):
             '; Whole-head T1 \n' \
             'use_implicit_mask       = 0 \n' \
             'use_mask_ref_scalar     = 1 1 1 1 1 1 1 \n' \
-            'use_mask_mov_scalar     = 0 0 0 0 0 0 0 \n' \
+            'use_mask_mov_scalar     = 1 1 1 1 1 1 1 \n' \
             'fwhm_ref_scalar         = 8.0 8.0 4.0 2.0 1.0 0.5 0.25 \n' \
             'fwhm_mov_scalar         = 8.0 8.0 4.0 2.0 1.0 0.5 0.25 \n' \
             'lambda_scalar           = 1 1 1 1 1 1 1 \n' \
@@ -477,8 +477,8 @@ def applyWarpWrapper(img_path, ref_path, warped_path, warp_path, interp='spline'
 #     return job_id
 
 
-def submitJob(name, log_dir, queue, wait_for=[], script=None, command=None, coprocessor_class=None, export_var=None,
-                  debug=False):
+def fslsubWrapper(name, log_dir, queue, wait_for=[], script=None, command=None, coprocessor_class=None,
+                  coprocessor=None, export_var=None, debug=False):
     """! Wrapper for fslsub - submits a job to the cluster. This function can be easily extended to work with other workload managers.
 
     @param name:                  Job name
@@ -493,23 +493,28 @@ def submitJob(name, log_dir, queue, wait_for=[], script=None, command=None, copr
 
     @return  The job ID.
     """
-    cmd = 'fsl_sub -n'
-    job_ids_bool = [job != '' for job in wait_for]
-    if wait_for and any(job_ids_bool):
-        cmd += ' -j '
-        wait_for_arr = np.array(wait_for)
-        wait_for_arr = wait_for_arr[job_ids_bool]
-        for j, job in enumerate(wait_for_arr):
-            cmd += job.replace("\n", "")
-            if j < len(wait_for_arr) - 1:
-                cmd += ','
+    cmd = 'fsl_sub'
+
+    if wait_for:
+        job_ids_bool = [job != '' for job in wait_for]
+        if any(job_ids_bool):
+            cmd += ' -j '
+            wait_for_arr = np.array(wait_for)
+            wait_for_arr = wait_for_arr[job_ids_bool]
+            for j, job in enumerate(wait_for_arr):
+                cmd += job.replace("\n", "")
+                if j < len(wait_for_arr) - 1:
+                    cmd += ','
 
     cmd += ' -N ' + name + \
            ' -l ' + log_dir + \
            ' -q ' + queue
 
-    if coprocessor_class is not None :
-        cmd += ' --coprocessor cuda'
+    if coprocessor_class is not None:
+        cmd += ' --coprocessor_class ' + coprocessor_class
+        cmd += ' --coprocessor_class_strict '
+    if coprocessor is not None:
+        cmd += ' --coprocessor ' + coprocessor + ' -R 32'
 
     if export_var is not None :
         cmd += ' --export ' + export_var
@@ -1348,7 +1353,7 @@ if __name__ == "__main__":
                             aff_ref_scalar = [tree.get('identity_mat')]
                             aff_mov_scalar = [tree.get('T1_to_MNI_mat')]
                             mask_ref_scalar = [img_ref_T1brain_mask_path]
-                            mask_mov_scalar = ['NULL']
+                            mask_mov_scalar = [tree.get('lesion_mask_in_T1')]
                             img_ref_tensor = []
                             img_mov_tensor = []
                             aff_ref_tensor = []
@@ -1387,7 +1392,7 @@ if __name__ == "__main__":
 
                 job_ids[28] = submitJob(tag+'_'+task_name, log_dir, script=script_path, queue=gpuq,
                                         wait_for=list(itemgetter(*[21, 23, 24, 25, 26, 27, 28, 44, 45, 46, 47, 48, 50])(job_ids)),
-                                        coprocessor_class='P',
+                                        coprocessor_class=None, coprocessor='cuda',
                                         export_var=export_var_str['SINGULARITY_BIND'], debug=False)
                 print('submitted: ' + task_name)
 

tempconfig/data.tree

@@ -6,3 +6,4 @@ ext_mat=.mat
         T1_orig{ext_nii} (T1_head)
         T1_brain{ext_nii} (T1_brain)
         T1_brain_mask{ext_nii} (T1_brain_mask)
+        T2Lesion_in_T1{ext_nii} (lesion_mask_in_T1)
\ No newline at end of file