Merge pull request #42 from niniko1997/master

-3T flag option
bids-apps · Aug 1, 2018 · 1d071d6 · 1d071d6
2 parents b63b6ce + 7530906
commit 1d071d6
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Showing 2 changed files with 31 additions and 1 deletion.
diff --git a/README.md b/README.md
@@ -41,7 +41,7 @@ This App has the following command line arguments:
                       [--measurements {area,volume,thickness,thicknessstd,meancurv,gauscurv,foldind,curvind}
                                       [{area,volume,thickness,thicknessstd,meancurv,gauscurv,foldind,curvind} ...]]
                       [-v] [--bids_validator_config BIDS_VALIDATOR_CONFIG]
-                      [--skip_bids_validator]
+                      [--skip_bids_validator] [--3T {true,false}]
                       bids_dir output_dir {participant,group1,group2}
 
         FreeSurfer recon-all + custom template generation.
@@ -127,6 +127,9 @@ This App has the following command line arguments:
                                 info
           --skip_bids_validator
                                 skips bids validation
+	  --3T {true,false}     enables the two 3T specific options that recon-all
+	  			supports: nu intensity correction params, and the 
+				special schwartz atlas
 
 #### Participant level
 To run it in participant level mode (for one participant):

diff --git a/run.py b/run.py
@@ -102,8 +102,15 @@ def run(command, env={}, ignore_errors=False):
 parser.add_argument('--skip_bids_validator',
                     help='skips bids validation',
                     action='store_true')
+parser.add_argument('--3T',
+                    help='enables the two 3T specific options that recon-all supports: nu intensity correction params, and the special schwartz atlas',
+                    choices = ['true', 'false'],
+                    default = 'true')
 args = parser.parse_args()
 
+
+three_T = vars(args)['3T']
+
 if args.bids_validator_config:
     run("bids-validator --config {config} {bids_dir}".format(
         config=args.bids_validator_config,
@@ -120,6 +127,7 @@ def run(command, env={}, ignore_errors=False):
 else:
     acq_tpl = "*"
 
+
 # if there are session folders, check if study is truly longitudinal by
 # searching for the first subject with more than one valid sessions
 multi_session_study = False
@@ -200,6 +208,10 @@ def run(command, env={}, ignore_errors=False):
                                                 "anat",
                                                 "%s_T1w.nii*" % acq_tpl))
                         input_args = ""
+
+                        if three_T == 'true':
+                            input_args += " -3T"
+
                         for T1 in T1s:
                             if (round(max(nibabel.load(T1).header.get_zooms()), 1) < 1.0 and args.hires_mode == "auto") or args.hires_mode == "enable":
                                 input_args += " -hires"
@@ -224,6 +236,8 @@ def run(command, env={}, ignore_errors=False):
 
                         fsid = "sub-%s_ses-%s" % (subject_label, session_label)
                         stages = " ".join(["-" + stage for stage in args.stages])
+
+
                         cmd = "recon-all -subjid %s -sd %s %s %s -openmp %d" % (fsid,
                                                                                           output_dir,
                                                                                           input_args,
@@ -254,6 +268,7 @@ def run(command, env={}, ignore_errors=False):
                     input_args = " ".join(["-tp %s" % tp for tp in timepoints])
                     fsid = "sub-%s" % subject_label
                     stages = " ".join(["-" + stage for stage in args.stages])
+
                     cmd = "recon-all -base %s -sd %s %s %s -openmp %d" % (fsid,
                                                                                     output_dir,
                                                                                     input_args,
@@ -280,6 +295,7 @@ def run(command, env={}, ignore_errors=False):
                         # longitudinally process all timepoints
                         fsid = "sub-%s" % subject_label
                         stages = " ".join(["-" + stage for stage in args.stages])
+
                         cmd = "recon-all -long %s %s -sd %s %s -openmp %d" % (tp,
                                                                                         fsid,
                                                                                         output_dir,
@@ -305,6 +321,10 @@ def run(command, env={}, ignore_errors=False):
                                         "anat",
                                         "%s_T1w.nii*" % acq_tpl))
                 input_args = ""
+
+                if three_T == 'true':
+                            input_args += " -3T"
+
                 for T1 in T1s:
                     if (round(max(nibabel.load(T1).header.get_zooms()), 1) < 1.0 and args.hires_mode == "auto") or args.hires_mode == "enable":
                         input_args += " -hires"
@@ -333,6 +353,7 @@ def run(command, env={}, ignore_errors=False):
 
                 fsid = "sub-%s" % subject_label
                 stages = " ".join(["-" + stage for stage in args.stages])
+
                 cmd = "recon-all -subjid %s -sd %s %s %s -openmp %d" % (fsid,
                                                                                   output_dir,
                                                                                   input_args,
@@ -369,7 +390,12 @@ def run(command, env={}, ignore_errors=False):
             if not T1s:
                 print("No T1w nii files found for subject %s. Skipping subject." % subject_label)
                 continue
+
             input_args = ""
+
+            if three_T == 'true':
+                            input_args += " -3T"
+
             for T1 in T1s:
                 if (round(max(nibabel.load(T1).header.get_zooms()), 1) < 1.0 and args.hires_mode == "auto") or args.hires_mode == "enable":
                     input_args += " -hires"
@@ -391,6 +417,7 @@ def run(command, env={}, ignore_errors=False):
 
             fsid = "sub-%s" % subject_label
             stages = " ".join(["-" + stage for stage in args.stages])
+
             cmd = "recon-all -subjid %s -sd %s %s %s -openmp %d" % (fsid,
                                                                               output_dir,
                                                                               input_args,