example running maxfilter on cluster

Author: cjayb

examples/maxfilter_on_cluster.py

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+from stormdb.access import Query
+from stormdb.process import Maxfilter
+from os.path import join
+from os import makedirs
+
+proj_name = 'MINDLAB2018_MEG-SF-Integration-Images'
+mf_out_path = join('/projects', proj_name, 'scratch', 'maxfiltered')
+log_out_path = join('/projects', proj_name, 'scratch', 'maxfiltered', 'logs')
+makedirs(log_out_path, exist_ok=True)
+
+qy = Query(proj_name)
+mf = Maxfilter(proj_name)
+
+# Get all series (regardless of subject) named '*SFtuned*' (note wildcards)
+series = qy.filter_series(description='*SFtuned*')
+# Restrict to specific subjects
+# series = qy.filter_series(description='*SFtuned*', subjects=['0007', '0012'])
+# Restrict to specific modality
+# series = qy.filter_series(description='*mprage*', modalities='MR')
+
+for ses in series:
+    # MEG acquistions will be split into 2GB chunks if long
+    for fifname in ses['files']:
+        in_fname = join(ses['path'], fifname)
+
+        outbase = splitext(fifname)[0]
+        out_fname = join(mf_out_path, outbase + '_tsss.fif')
+        log_fname = join(log_out_path, outbase + '_tsss.log')
+
+        # see maxfilter manual for options
+        mf.build_cmd(in_fname, out_fname, logfile=log_fname,
+                autobad='on', st=True, st_buflen=16.0, st_corr=0.96,
+                force=False)
+
+mf.submit(fake=True)  # remove "fake" when ready to submit!
+
+# mf.commands contains a list of commands that will be sent to cluster