Merge pull request #17 from Hyedryn/tracking_fix

Tracking fix
Hyedryn · Apr 21, 2023 · 4bc7011 · 4bc7011
2 parents 0c4404c + b98d6ae
commit 4bc7011
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Showing 2 changed files with 2 additions and 5 deletions.
diff --git a/elikopy/core.py b/elikopy/core.py
@@ -983,7 +983,7 @@ def odf_msmtcsd(self, folder_path=None, num_peaks = 2, peaks_threshold=0.25, mas
         f.close()
 
 
-    def tracking(self, folder_path=None, streamline_number:int=100000, max_angle:int=15, cutoff:float=0.1, msmtCSD:bool=True, output_filename:str=None,
+    def tracking(self, folder_path=None, streamline_number:int=100000, max_angle:int=15, cutoff:float=0.1, msmtCSD:bool=True, output_filename:str="tractogram",
                  slurm=None, patient_list_m=None, slurm_email=None, slurm_timeout=None, cpus=None, slurm_mem=None):
         """Computes the odf using MSMT-CSD for each subject. The outputs are available in the directories <folder_path>/subjects/<subjects_ID>/dMRI/tractography/.
 

diff --git a/elikopy/individual_subject_processing.py b/elikopy/individual_subject_processing.py
@@ -3463,7 +3463,7 @@ def print_page(self, images):
 
 def tracking_solo(folder_path:str, p:str, streamline_number:int=100000,
                   max_angle:int=15, cutoff:float=0.1, msmtCSD:bool=True,
-                  output_filename:str=None,core_count:int=1):
+                  output_filename:str='tractogram',core_count:int=1):
     """ Computes the whole brain tractogram of a single patient based on the fod obtained from msmt-CSD.
 
     :param folder_path: the path to the root directory.
@@ -3503,9 +3503,6 @@ def tracking_solo(folder_path:str, p:str, streamline_number:int=100000,
     mask_path = folder_path + '/subjects/' + patient_path + '/masks/' + patient_path + "_brain_mask_dilated.nii.gz"
     dwi_path = folder_path + '/subjects/' + patient_path + '/dMRI/preproc/' + patient_path + '_dmri_preproc.nii.gz'
 
-    if not output_filename:
-        output_filename='tractogram'
-
     output_file = tracking_path+patient_path+'_'+output_filename+'.tck'
 
     if not os.path.isdir(tracking_path):