nipype_preproc_spm_abide_maxmun.py: sample script for preprocessing ABIDE MaxMun dataset

dohmatob · dohmatob · commit a91a34b4a01e · 2012-12-06T15:52:22.000+01:00
diff --git a/nipype_preproc_spm_abide_maxmun.py b/nipype_preproc_spm_abide_maxmun.py
@@ -0,0 +1,71 @@
+"""
+:Module: nipype_preproc_spm_nyu
+:Synopsis: SPM use-case for preprocessing ABIDE MAxMun rest dataset
+:Author: dohmatob elvis dopgima
+
+"""
+
+# standard imports
+import os
+import glob
+import sys
+
+# import spm preproc utilities
+import nipype_preproc_spm_utils
+
+DATASET_DESCRIPTION = """\
+<p>ABIDE MaxMun dataset</p>\
+"""
+
+if __name__ == '__main__':
+    # sanitize cmd-line input
+    if len(sys.argv)  < 3:
+        print "\r\nUsage: python %s <path_to_ABIDE_folder> <output_dir>\r\n" \
+            % sys.argv[0]
+        print "Example:\r\npython %s ~/ABIDE ~/ABIDE_runs/MaxMun" % sys.argv[0]
+        sys.exit(1)
+
+    ABIDE_DIR = os.path.abspath(sys.argv[1])
+
+    OUTPUT_DIR = os.path.abspath(sys.argv[2])
+    if not os.path.isdir(OUTPUT_DIR):
+        os.makedirs(OUTPUT_DIR)
+
+    # glob for MaxMun subject_ids
+    subject_ids = [os.path.basename(x)
+                   for x in glob.glob(
+            os.path.join(ABIDE_DIR, "MaxMun_*/MaxMun_*"))]
+
+    # producer for MaxMun subjects
+    def subject_factory():
+        for subject_id in subject_ids:
+            subject_data = nipype_preproc_spm_utils.SubjectData()
+            subject_data.subject_id = subject_id
+            subject_data.session_id = 'UNKNOWN_SESSION'
+
+            subject_data.func = glob.glob(
+                os.path.join(
+                    ABIDE_DIR,
+                    "%s/%s/scans/rest/resources/NIfTI/files/rest.nii" % (
+                        subject_id, subject_id)))
+
+            subject_data.anat = glob.glob(
+                os.path.join(
+                    ABIDE_DIR,
+                    "%s/%s/scans/anat/resources/NIfTI/files/mprage.nii" % (
+                        subject_id, subject_id)))
+
+            subject_data.output_dir = os.path.join(
+                os.path.join(
+                    OUTPUT_DIR, subject_data.session_id),
+                subject_id)
+
+            yield subject_data
+
+    # do preprocessing proper
+    report_filename = os.path.join(OUTPUT_DIR,
+                                   "_report.html")
+    nipype_preproc_spm_utils.do_group_preproc(
+        subject_factory(),
+        dataset_description=DATASET_DESCRIPTION,
+        report_filename=report_filename)
