ENH: Added stand alone Freesurfer processing.

AutoWorkup/CreateFreeSufereScripts.py

@@ -0,0 +1,121 @@
+__author__ = 'johnsonhj'
+
+
+import os
+import SessionDB
+
+## GLOBALS ARE EVIL, but so is searching for all the items necessary to complete an analysis
+
+FREESURFER_HOME='/Shared/sinapse/sharedopt/20131115/RHEL6/freesurfer'
+#subjects_dir='/Shared/sinapse/CACHE/TRACKON_FS20131220'
+subjects_dir='/Shared/sinapse/CACHE/TRACKON_FS20131220_NoT2'
+scripts_dir = os.path.join(subjects_dir,'scripts')
+if not os.path.exists(scripts_dir):
+    os.makedirs(scripts_dir)
+
+subject_data_file='/Shared/johnsonhj/HDNI/20131116_TrackOn/scripts/edited_without_T2_PD_15s_track_autoworkup_TRACKON.csv'
+subjectDatabaseFile=os.path.join(scripts_dir,'subject_inputs.db')
+
+single_subject=['all']
+#single_subject=['012366774']
+mountPrefix=''
+
+if (not os.path.exists(subjectDatabaseFile)) or (
+        os.path.getmtime(subjectDatabaseFile) < os.path.getmtime(subject_data_file)):
+    ExperimentDatabase = SessionDB.SessionDB(subjectDatabaseFile, single_subject)
+    ExperimentDatabase.MakeNewDB(subject_data_file, mountPrefix)
+    ExperimentDatabase = None
+    ExperimentDatabase = SessionDB.SessionDB(subjectDatabaseFile, single_subject)
+else:
+    print("Single_subject {0}: Using cached database, {1}".format(single_subject,subjectDatabaseFile))
+    ExperimentDatabase = SessionDB.SessionDB(subjectDatabaseFile, single_subject)
+
+all_sessions=ExperimentDatabase.getAllSessions()
+
+print "sessions: ",all_sessions
+
+def find_mgz(inlist):
+    outlist = list()
+    for ff in inlist:
+        testmgz=ff.replace('.nii.gz','.mgz')
+        if os.path.exists(testmgz):
+            outlist.append(testmgz)
+        else:
+            outlist.append(ff)
+    return outlist
+
+def mkfsscript(session,outscript,t1list,t2list):
+
+    T1_FLAGS=''
+    for t1 in t1list:
+        T1_FLAGS+= " -i " + t1
+
+    T2_FLAGS=''
+    if len(t2list) > 0 and subjects_dir == '/Shared/sinapse/CACHE/TRACKON_FS20131220' :
+        ## HACK:  Rachael requested that this NOT be used
+        T2_FLAGS=' -T2 '+ t2list[0]
+        pass
+
+    auto_recon_script = """#!/bin/bash
+#$ -o {FSSUBJDIR}/scripts/base_{SUBJ_SESSION_ID}_qsub.out
+#$ -e {FSSUBJDIR}/scripts/base_{SUBJ_SESSION_ID}_qsub.err
+#$ -cwd
+mkdir -p {FSSUBJDIR}/scripts/
+export FREESURFER_HOME={FSHOME}
+export SUBJECTS_DIR={FSSUBJDIR}
+
+source {FSHOME}/FreeSurferEnv.sh
+
+MAX_SLOTS=$NSLOTS
+if [ -z "$MAX_SLOTS" ]; then
+  MAX_SLOTS=2
+fi
+
+rm -f {FSSUBJDIR}/{SUBJ_SESSION_ID}/scripts/IsRunning.lh+rh
+if [ ! -f {FSSUBJDIR}/{SUBJ_SESSION_ID}/mri/orig/001.mgz ]; then
+  #Some data sets have FOV greater than 256mm, so force clipping to 256 with the -cw flag
+  {FSHOME}/bin/recon-all -3T -debug -openmp $MAX_SLOTS  -subjid {SUBJ_SESSION_ID} {T1_FLAGS} {T2_FLAGS} -cw256
+fi
+
+{FSHOME}/bin/recon-all -3T -debug -openmp $MAX_SLOTS  -subjid {SUBJ_SESSION_ID} {T2_FLAGS} -make autorecon1
+recon1_stats=$?
+if [ $recon1_stats -eq 0 ];then
+  {FSHOME}/bin/recon-all -3T -debug -openmp $MAX_SLOTS  -subjid {SUBJ_SESSION_ID} {T2_FLAGS} -make autorecon2
+  recon2_stats=$?
+  if [ $recon2_stats -eq 0 ];then
+    {FSHOME}/bin/recon-all -3T -debug -openmp $MAX_SLOTS  -subjid {SUBJ_SESSION_ID} {T2_FLAGS} -make autorecon3
+    recon3_stats=$?
+      if [ $recon3_stats -eq 0 ];then
+        {FSHOME}/bin/recon-all -3T -debug -openmp $MAX_SLOTS  -subjid {SUBJ_SESSION_ID} {T2_FLAGS} -make qcache
+        qcache_stats=$?
+      else
+        echo "SKIPPING STAGE3 because STAGE2 failed"
+      fi
+  else
+    echo "SKIPPING STAGE3 because STAGE2 failed"
+  fi
+else
+  echo "SKIPPING STAGE2 because STAGE1 failed"
+fi
+
+status=$?
+exit $status
+""".format(
+           FSHOME=FREESURFER_HOME,
+           FSSUBJDIR=subjects_dir,
+           SUBJ_SESSION_ID=session,
+           T1_FLAGS=T1_FLAGS,T2_FLAGS=T2_FLAGS)
+    outfd = open(outscript,'w')
+
+    outfd.write(auto_recon_script)
+
+for session in all_sessions:
+    T1_files=ExperimentDatabase.getFilenamesByScantype(session,['T1-30'])
+    T2_files=ExperimentDatabase.getFilenamesByScantype(session,['T2-30'])
+
+    T1_files=find_mgz(T1_files)
+    T2_files=find_mgz(T2_files)
+    print T1_files
+    print T2_files
+    fsscript = os.path.join(scripts_dir,'fs'+session+'.sh')
+    mkfsscript(session,fsscript,T1_files,T2_files)