upgraded to new version of Filetree

config/MS_template.tree

@@ -3,9 +3,9 @@ ext_mat=.mat
 ext_ini=.ini
 ext_txt=.txt
 
-{data_dir}
+!{data_dir}
     ->data (data)
-{template_dir}
+!{template_dir}
     misc (misc_dir)
         ident{ext_mat} (identity_mat)
     log (log_dir)
@@ -69,6 +69,7 @@ ext_txt=.txt
             nln_template_T1_brain_mask_{step_id}_{it_id}{ext_nii} (T1_brain_mask_nln_template)
             nln_template_T1_brain_mask_weighted_{step_id}_{it_id}{ext_nii} (T1_brain_mask_weighted_nln_template)
             nln_template_T1_brain_SD_{step_id}_{it_id}{ext_nii} (T1_brain_SD_nln_template)
+            nln_template_T1_head_SD_{step_id}_{it_id}{ext_nii} (T1_head_SD_nln_template)
             nln_template_T1_head_{step_id}_{it_id}{ext_nii} (T1_head_nln_template)
             nln_template_T2_head_{step_id}_{it_id}{ext_nii} (T2_head_nln_template)
             nln_template_DTI_{step_id}_{it_id}{ext_nii} (DTI_nln_template)

run_template_construction.py

@@ -15,8 +15,8 @@ import nibabel as nib
 import numpy as np
 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.filetree import FileTree
+from file_tree import FileTree
+# from fsl.utils.filetree import FileTree
 from fsl.utils.fslsub import func_to_cmd
 from operator import itemgetter
 import tempfile
@@ -433,7 +433,6 @@ def submitJob(name, log_dir, queue, wait_for=[], script=None, command=None, copr
 
     @return  The job ID.
     """
-
     cmd = 'fsl_sub'
     if wait_for and any(job != '' for job in wait_for):
         cmd += ' -j '
@@ -466,7 +465,6 @@ def submitJob(name, log_dir, queue, wait_for=[], script=None, command=None, copr
 
     return job_id
 
-
 def RMSdifference(img1_path, img2_path, mask1_path=None, mask2_path=None, rms_path=None):
     """! Calculates the difference between two images or warps as the root mean squared (RMS)
 
@@ -748,7 +746,7 @@ if __name__ == "__main__":
     os.mkdir(base_dir, mode=0o700) if not os.path.exists(base_dir) else print(base_dir + ' exists')
     os.chmod(base_dir, 0o700)
 
-    tree = FileTree.read(tree_path, directory='')
+    tree = FileTree.read(tree_path, top_level='')
     tree = tree.update(data_dir=data_dir, template_dir=base_dir)
 
     script_dir = tree.get('script_dir')
@@ -1215,7 +1213,7 @@ if __name__ == "__main__":
                     img_ref_T1brain_path = tree.get('T1_brain_affine_template')
                     img_ref_T1head_path = tree.get('T1_head_affine_template')
                     img_ref_T2head_path = tree.get('T2_head_affine_template')
-                    img_ref_tensor_path = tree.get('DTI_tensor_affine_template')
+                    img_ref_tensor_path = tree.get('T1_head_affine_template')
                     img_ref_T1brain_mask_path = tree.get('T1_brain_mask_weighted_affine_template')
                 else:
                     if it == 1:
@@ -1229,7 +1227,7 @@ if __name__ == "__main__":
                     img_ref_T1brain_path = tree.get('T1_brain_nln_template')
                     img_ref_T1head_path = tree.get('T1_head_nln_template')
                     img_ref_T2head_path = tree.get('T2_head_nln_template')
-                    img_ref_tensor_path = tree.get('DTI_tensor_nln_template')
+                    img_ref_tensor_path = tree.get('T1_head_nln_template')
                     img_ref_T1brain_mask_path = tree.get('T1_brain_mask_weighted_nln_template')
                     avgwarp_prev_it_path = tree.get('avg_warp')
                     avgmask_prev_it_path = tree.get('T1_brain_mask_nln_template')
@@ -1706,7 +1704,7 @@ if __name__ == "__main__":
                                          tmp_dir=script_dir, kwargs=None,
                                          clean="never")
                     job_ids[52] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq,
-                                                wait_for=[job_ids[44]])
+                                                wait_for=list(itemgetter(*[44,49])(job_ids)))
                     print('submitted: ' + task_name)
 
 # RMS of intensity standard deviation of individual images in template space
@@ -1718,14 +1716,14 @@ if __name__ == "__main__":
                     img_paths.append(tree.get('warped_T1brain'))
 
                 jobcmd = func_to_cmd(RMSstandardDeviation, args=(img_paths,
-                                                                 tree.get('T1_brain_nln_template'),
+                                                                 tree.get('T1_head_nln_template'),
                                                                  tree.get('T1_brain_mask_nln_template'),
-                                                                 tree.get('T1_brain_SD_nln_template'),
+                                                                 tree.get('T1_head_SD_nln_template'),
                                                                  tree.get('sd_intensity_output')),
                                      tmp_dir=script_dir, kwargs=None,
                                      clean="never")
                 job_ids[53] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq,
-                                            wait_for=[job_ids[44]])
+                                            wait_for=list(itemgetter(*[45, 49])(job_ids)))
                 print('submitted: ' + task_name)