Fixing a bug in the FreeSurfer call

bip/ext_wrappers/freesurfer.py

@@ -28,11 +28,11 @@ def recon_all(subjects_dir, directive, subjid, infile, FLAIR=None, **kwargs):
 
     os.environ["SUBJECTS_DIR"] = subjects_dir
 
-    cmd = ['recon-all', "-"+directive + " -s " + subjid ]
-    cmd += [ " -i " + subjects_dir + "/" + infile ]
+    cmd = ['recon-all', "-" + directive + " -s " + subjid]
+    cmd += [" -i " + subjects_dir + "/" + infile]
 
     if FLAIR:
-        cmd += [ " -FLAIR " + subjects_dir + "/" + FLAIR + " -FLAIRpial" ]
+        cmd += [" -FLAIR " + subjects_dir + "/" + FLAIR + " -FLAIRpial -debug"]
 
     return cmd
 

bip/pipelines/struct_FS/FS_proc.py

@@ -11,9 +11,11 @@
 #
 
 import os
+import shutil
 import logging
+import subprocess
 from pipe_tree import In, Out, Ref
-from bip import ext_wrappers
+#from bip import ext_wrappers
 from bip.utils import redirect_logging
 
 log = logging.getLogger(__name__)
@@ -22,15 +24,31 @@ def run(ctx,
         T1_unbiased:                In,
         T2_FLAIR_unbiased:          In(optional=True),
         logs_dir:                   Ref,
+        FreeSurfer_dir:             Ref,
         rh_entorhinal_exvivo_label: Out):
 
     with redirect_logging('FS_proc', outdir=logs_dir):
-        opt_T2_FLAIR = None
+
+        if os.path.exists(FreeSurfer_dir):
+            shutil.rmtree(FreeSurfer_dir)
+
+        subjects_dir=os.getcwd()
+
+        os.environ["SUBJECTS_DIR"] = subjects_dir + "/" + ctx.subject
+        cmd = 'recon-all -all -s FreeSurfer -i ' + subjects_dir + "/" + T1_unbiased
 
         if os.path.exists(T2_FLAIR_unbiased):
-            opt_T2_FLAIR = T2_FLAIR_unbiased
+            cmd += " -FLAIR " + subjects_dir + "/" + T2_FLAIR_unbiased + " -FLAIRpial"
+
+        try:
+            returned_val = subprocess.call(cmd, shell=True)
+            print(returned_val)
+        except Exception as e:
+            print('Command: ' + cmd)
+            print('Exception type: \t' + str(type(e)))
+            print('Exception args: \t' + str(e.args))
+            print('Exception message: \t' + str(e))
 
-        ext_wrappers.recon_all(subjects_dir=os.getcwd(), directive="all",
-                               subjid="FreeSurfer", infile=T1_unbiased,
-                               FLAIR=opt_T2_FLAIR)
-        print("PATATA")
+        #ext_wrappers.recon_all(subjects_dir=os.getcwd(),
+        #                       directive="all", subjid="FreeSurfer",
+        #                       infile=T1_unbiased, FLAIR=opt_T2_FLAIR)