Changed masking to mean and threshold to 0.5

run_template_construction.py

@@ -17,12 +17,11 @@ import sys
 from fsl.wrappers import fslmaths,flirt,applyxfm,concatxfm,bet,fast,fslstats
 from fsl.wrappers.fnirt import invwarp, applywarp, convertwarp
 from file_tree import FileTree
-from fsl.utils.fslsub import func_to_cmd
 from operator import itemgetter
 import tempfile
 import argparse
+from fsl.utils.fslsub import func_to_cmd
 import fsl_sub
-import logging
 
 def writeConfig(step,mod,fpath):
     """! Writes the nonlinear registration parameters for a given resolution level and modalities to a file readable by MMORF.
@@ -535,19 +534,19 @@ def submitJob(command, name, log_dir, queue, wait_for=None, array_task=False, co
                 hold_ids.append(job_id)
 
     job_id = fsl_sub.submit(command=command,
-                   array_task=array_task,
-                   jobhold=hold_ids,
-                   name=name,
-                   logdir=log_dir,
-                   queue=queue,
-                   coprocessor=coprocessor,
-                   coprocessor_class=coprocessor_class,
-                   coprocessor_class_strict=coprocessor_class_strict,
-                   coprocessor_multi=coprocessor_multi,
-                   threads=threads,
-                   export_vars=export_var,
-                   jobram=jobram,
-                   jobtime=jobtime
+                            array_task=array_task,
+                            jobhold=hold_ids,
+                            name=name,
+                            logdir=log_dir,
+                            queue=queue,
+                            coprocessor=coprocessor,
+                            coprocessor_class=coprocessor_class,
+                            coprocessor_class_strict=coprocessor_class_strict,
+                            coprocessor_multi=coprocessor_multi,
+                            threads=threads,
+                            export_vars=export_var,
+                            jobram=jobram,
+                            jobtime=jobtime
                    )
 
     return str(job_id)
@@ -814,8 +813,6 @@ def mmorfWrapper(mmorf_run_cmd, config_path, img_warp_space,
 if __name__ == "__main__":
     """! Main function submitting the jobs.
     """
-    logging.basicConfig()
-    logging.getLogger('fsl.wrappers').setLevel(logging.DEBUG)
 
     mni_path = os.getenv('FSLDIR')+'/data/standard/MNI152lin_T1_1mm_brain.nii.gz'
     identity_path = os.getenv('FSLDIR')+'/etc/flirtsch/ident.mat'
@@ -900,7 +897,7 @@ if __name__ == "__main__":
     jobram_low = 4
     jobram_hi = 12
 
-    jobtime_low = 15
+    jobtime_low = 20
     jobtime_high = 60
 
     job_ids = ['' for _ in range(100)]
@@ -955,7 +952,7 @@ if __name__ == "__main__":
                 tree = tree.update(sub_id=id)
                 T1_head_path = tree.get(mod['T1_head_key'])
                 T1_clamped_path = tree.get('T1_head_clamped', make_dir=True)
-                T1_clamped_hard_path = tree.get('T1_head_clamped_hard')
+                T1_clamped_hard_path = tree.get('T1_head_clamped_hard', make_dir=True)
 
                 jobcmd = func_to_cmd(run_soft_clamp,
                                      args=(T1_head_path, T1_clamped_path),
@@ -1305,7 +1302,7 @@ if __name__ == "__main__":
             print('submitted: ' + task_name)
 
             task_name = '{:03d}_affT_create_weighted_brain_mask'.format(task_count)
-            jobcmd = 'fslmaths ' + aff_template_path + ' -thr 0.1 -bin -mul 7 -add 1 -inm 1 ' + tree.get('T1_brain_mask_weighted_affine_template')
+            jobcmd = 'fslmaths ' + aff_template_path + ' -thr 0.5 -bin -mul 7 -add 1 -inm 1 ' + tree.get('T1_brain_mask_weighted_affine_template')
             # job_ids[23] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[22]])
             job_ids[23] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[22]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)
             print('submitted: ' + task_name)
@@ -1854,7 +1851,7 @@ if __name__ == "__main__":
                     img_paths.append(tree.get('warped_T1brain_mask'))
                 nln_template_path = tree.get('T1_brain_mask_nln_template')
 
-                jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'intersection', False), tmp_dir=script_dir,
+                jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'mean', False), tmp_dir=script_dir,
                                      kwargs=None, clean="never")
                 # job_ids[49] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[38]])
                 job_ids[49] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[38]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)
@@ -1862,7 +1859,7 @@ if __name__ == "__main__":
 
                 task_count += 1
                 task_name = '{:03d}_nlnT_average_T1_brain_mask_weighted'.format(task_count)
-                jobcmd = 'fslmaths ' + nln_template_path + ' -thr 0.1 -bin -mul 7 -add 1 -inm 1 ' + tree.get(
+                jobcmd = 'fslmaths ' + nln_template_path + ' -thr 0.5 -bin -mul 7 -add 1 -inm 1 ' + tree.get(
                     'T1_brain_mask_weighted_nln_template')
                 # job_ids[50] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[49]])
                 job_ids[50] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[49]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)