wrapper.ipynb

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    "%reset -f\n",
    "import os\n",
    "from glob import glob\n",
    "import re #regular expression\n",
    "import datetime"
   ]
  },
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    "## Args\n",
    "model=121\n",
    "task_list=[6]\n",
    "subj_wild = 'voice875*' #'voice*'\n",
    "hpfilter=120\n",
    "\n",
    "# user specific\n",
    "fmri_py_script='/om/user/gr21783/git/openfmri/subject_level/fmri_ants_openfmri_sparse.py'\n",
    "work_dir_base='/om/scratch/Wed/gr21783/voice20151111'\n",
    "crashdump_base='/home/gr21783/OMerrLog'\n",
    "out_dir_base = '/om/project/voice/processedData/l1analysis/l1output_20151106'\n",
    "\n",
    "# leave alone\n",
    "file_path_openfmri='/om/project/voice/processedData/openfmri'\n",
    "targetTemplate='/om/project/voice/processedData/resting/templates/OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz'\n",
    "fsdata_base='/om/project/voice/processedData/fsdata'\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "# Copy this file and the workflow script to the output directory\n",
    "#mkdir -p $out_dir\n",
    "#cp submit_sparseL1.sh $out_dir\n",
    "#cp $fmri_py_script $out_dir"
   ]
  },
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     "text": [
      "['/om/project/voice/processedData/openfmri/participant_models/model200/voice987/session001_visit001/voice987_task001_run001_pataka', '/om/project/voice/processedData/openfmri/participant_models/model200/voice987/session001_visit001/voice987_task001_run002_pataka']\n",
      "['/om/project/voice/processedData/openfmri/participant_models/model200/voice987/session001/voice987_task001', '/om/project/voice/processedData/openfmri/participant_models/model200/voice987/session001/voice987_task001']\n",
      "\n",
      "['/om/project/voice/processedData/openfmri/participant_models/model200/voice987/session001/voice987_task001']\n",
      "\n"
     ]
    }
   ],
   "source": [
    "#  Key idea:  Only loop over sessions that have specified model onsets, T1, and functional data\n",
    "file_list = []\n",
    "for task in task_list:\n",
    "    file_list.extend(glob(os.path.join(file_path_openfmri, 'participant_models', 'model%03d' % model,\n",
    "                                        subj_wild, 'session*', '*_task%03d_*' % task)))\n",
    "\n",
    "print file_list\n",
    "\n",
    "#  Make list unique based on session, since openfmri globs over visits\n",
    "#  Replace session###_visit### with session###\n",
    "#  Replace_run# with ''\n",
    "file_list = [re.sub('_visit\\d+', '', i) for i in file_list]\n",
    "file_list = [re.sub('_run\\d+_[a-z]+', '', i) for i in file_list]\n",
    "print file_list\n",
    "            \n",
    "print\n",
    "file_list = list(set(file_list))  # remove duplicate entries now that visit and run are gone\n",
    "file_list.sort()\n",
    "print file_list\n",
    "\n",
    "print\n",
    "\n"
   ]
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     "text": [
      "sbatch openfmriL1_1subj1task.sh /om/user/gr21783/git/openfmri/subject_level/fmri_ants_openfmri_sparse.py voice987 session001 /om/project/voice/processedData/fsdata/voice987/session001 200 /om/project/voice/processedData/l1analysis/l1output_20151106/model200/task001 /om/project/voice/processedData/openfmri /om/project/voice/processedData/resting/templates/OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz /om/scratch/Wed/gr21783/voice20151106/model200/task001/voice987 120 1 /home/gr21783/OMerrLog/task001_2015110609/voice987/session001\n"
     ]
    }
   ],
   "source": [
    "#  Remove if no T1 for given subject, session tuple\n",
    "for idx, text in enumerate(file_list):\n",
    "    try:       \n",
    "        subj = re.search('voice\\d+', text).group(0)\n",
    "    except AttributeError:\n",
    "        # AAA, ZZZ not found in the original string\n",
    "        subj = '' # apply your error hand\n",
    "    \n",
    "    try:       \n",
    "        session = re.search('session\\d+', text).group(0)\n",
    "    except AttributeError:\n",
    "        # AAA, ZZZ not found in the original string\n",
    "        session = '' # apply your error hand    \n",
    "    \n",
    "    try:       \n",
    "        task = re.search('task\\d+', text).group(0)\n",
    "    except AttributeError:\n",
    "        # AAA, ZZZ not found in the original string\n",
    "        task = '' # apply your error hand      \n",
    "    task = int(task[4:])\n",
    "    \n",
    "    \n",
    "    out_dir=os.path.join(out_dir_base,\n",
    "                     'model%03d' % model, 'task%03d' % task)\n",
    "    \n",
    "    file_path_anatomy_T1 = glob(os.path.join(file_path_openfmri, subj, session + '*', 'anatomy', '*T1w*.nii.gz'))\n",
    "    # If there are multiple anatomy folders, check each one for a *T1w*.nii.gz\n",
    "    if file_path_anatomy_T1:\n",
    "        # proceed to processing\n",
    "        fsdata_dir=os.path.join(fsdata_base, subj, session)\n",
    "\n",
    "        crashdump_dir=os.path.join(crashdump_base, 'task%03d_%s' % \n",
    "                                   (task, datetime.datetime.now().strftime('%Y%m%d%H')), subj, session)\n",
    "\n",
    "        workingDir=os.path.join(work_dir_base, 'model%03d' % model, 'task%03d' % task, subj)\n",
    "\n",
    "\n",
    "        #echo openfmriL1_1subj1task.sh $fmri_py_script $subj $session $fsdata_dir $model ${out_dir} $file_path_openfmri $targetTemplate $workingDir $hpfilter $task $crashdump_dir\n",
    "\n",
    "        cmd_str = 'sbatch openfmriL1_1subj1task.sh ' + fmri_py_script +  ' ' + subj  +  ' ' + session \\\n",
    "            + ' ' + fsdata_dir + ' ' + str(model) + ' ' + out_dir + ' '  + file_path_openfmri + ' ' +  \\\n",
    "            targetTemplate  + ' '  + workingDir  + ' '  +  str(hpfilter)  + ' '  +  str(task)   + ' '  +\\\n",
    "            crashdump_dir\n",
    "\n",
    "\n",
    "        print cmd_str   \n",
    "        os.system(cmd_str)\n",
    "    else:\n",
    "        print '*** NO T1 PRESENT ***:  ' + subj + ' ' + session \n",
    "        "
   ]
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