Conte_cifti.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Load libraries & helper functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from helpers import *\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Declare parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['CC0003', 'CC0005', 'CC0006', 'CC0007', 'CC0008', 'CC0010', 'CC0011', 'CC0012', 'CC0014', 'CC0024', 'CC0025', 'CC0027', 'CC0029', 'CC0033', 'CC0041', 'CC0046', 'CC0049', 'CC0056', 'CC0058', 'CC0059', 'CC0060', 'CC0061', 'CC0063', 'CC0064', 'CC0065', 'CC0068', 'CC0069', 'CC0070', 'CC0071', 'CC0074', 'CC0076', 'CC0077', 'CC0078', 'CC0079', 'CC0080', 'CC0081', 'CC0082', 'CC0085', 'CC0087', 'CC0088', 'CC0089', 'CC0091', 'CC0092', 'CC0096', 'CC0100', 'CC0101', 'CC0104', 'CC0105', 'CC0106', 'CC0108', 'CC0110', 'CC0111', 'CC0112', 'CC0114', 'CC0115', 'CC0116', 'CC0117', 'CC0118', 'CC0124', 'CC0126']\n"
     ]
    }
   ],
   "source": [
    "config.DATADIR                 = '/home/duboisjx/mnt10/LabUsers/duboisjx/data/Conte/MRI'\n",
    "config.pipelineName            = 'preGLM0'\n",
    "# fMRI runs\n",
    "fmriRuns                       = ['movie_1','movie_2','LOI1_1','LOI2_1','socnsLOI1_1','socnsLOI2_1']\n",
    "# use volume or surface data\n",
    "config.useNative               = False\n",
    "config.fmriFileTemplate        = '#fMRIrun#_Atlas.dtseries.nii'\n",
    "# config.fmriFileTemplate        = '#fMRIrun#.nii.gz'\n",
    "config.melodicFolder           = op.join('#fMRIrun#_hp2000.ica','filtered_func_data.ica') #the code #fMRIrun# will be replaced\n",
    "config.movementRelativeRMSFile = 'Movement_RelativeRMS.txt'\n",
    "config.movementRegressorsFile  = 'Movement_Regressors_dt.txt'\n",
    "\n",
    "tmp = config.fmriFileTemplate.split('.')\n",
    "if tmp[1]=='nii':\n",
    "    config.isCifti = False\n",
    "    config.parcellationName        = 'shen2013'\n",
    "    config.parcellationFile        = '/home/duboisjx/mnt10/LabUsers/duboisjx/data/parcellations/shenetal_neuroimage2013_new/shen_2.5mm_268_parcellation.nii.gz'\n",
    "    config.nParcels                = 268\n",
    "elif tmp[1]=='dtseries':\n",
    "    config.isCifti = True\n",
    "    config.parcellationName        = 'Glasser'\n",
    "    config.parcellationFile        = '/home/duboisjx/mnt10/LabUsers/duboisjx/data/parcellations/Glasser2016/Parcels.dlabel.nii'\n",
    "    config.nParcels                = 360\n",
    "else:\n",
    "    print 'unknown file extension'\n",
    "\n",
    "config.preWhitening            = False\n",
    "config.maskParcelswithAll      = True\n",
    "config.maskParcelswithGM       = False\n",
    "if config.maskParcelswithGM:\n",
    "    config.parcellationName    = config.parcellationName + '_GM'\n",
    "\n",
    "# submit jobs with sge\n",
    "config.queue        = False\n",
    "launchSubproc       = True\n",
    "parallelEnvironment = 'smp' #'openmp'\n",
    "    \n",
    "subjects  = [s for s in sorted(os.listdir(config.DATADIR)) if len(s)==6 and s[0:2]=='CC']\n",
    "print subjects"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Do work"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false,
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "submitted sCC0003_movie_1_preGLM0_ciftiTrue_20180511151514388\n",
      "submitted sCC0003_movie_2_preGLM0_ciftiTrue_20180511151515132\n",
      "submitted sCC0006_movie_1_preGLM0_ciftiTrue_20180511151516434\n",
      "submitted sCC0006_movie_2_preGLM0_ciftiTrue_20180511151517411\n",
      "submitted sCC0006_LOI2_1_preGLM0_ciftiTrue_20180511151518191\n",
      "submitted sCC0006_socnsLOI1_1_preGLM0_ciftiTrue_20180511151518937\n",
      "submitted sCC0006_socnsLOI2_1_preGLM0_ciftiTrue_20180511151519411\n",
      "submitted sCC0007_movie_1_preGLM0_ciftiTrue_20180511151520665\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0007_movie_2_preGLM0_ciftiTrue_20180511152922785\n",
      "submitted sCC0007_LOI1_1_preGLM0_ciftiTrue_20180511152923411\n",
      "submitted sCC0007_LOI2_1_preGLM0_ciftiTrue_20180511152923899\n",
      "submitted sCC0007_socnsLOI1_1_preGLM0_ciftiTrue_20180511152924497\n",
      "submitted sCC0007_socnsLOI2_1_preGLM0_ciftiTrue_20180511152925196\n",
      "submitted sCC0008_movie_1_preGLM0_ciftiTrue_20180511152925940\n",
      "submitted sCC0008_movie_2_preGLM0_ciftiTrue_20180511152926745\n",
      "submitted sCC0008_LOI1_1_preGLM0_ciftiTrue_20180511152927649\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 7 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0008_LOI2_1_preGLM0_ciftiTrue_20180511154028478\n",
      "submitted sCC0008_socnsLOI1_1_preGLM0_ciftiTrue_20180511154028602\n",
      "submitted sCC0008_socnsLOI2_1_preGLM0_ciftiTrue_20180511154028828\n",
      "submitted sCC0012_movie_1_preGLM0_ciftiTrue_20180511154029042\n",
      "submitted sCC0012_movie_2_preGLM0_ciftiTrue_20180511154029259\n",
      "submitted sCC0012_LOI1_1_preGLM0_ciftiTrue_20180511154029435\n",
      "submitted sCC0012_LOI2_1_preGLM0_ciftiTrue_20180511154029571\n",
      "submitted sCC0012_socnsLOI1_1_preGLM0_ciftiTrue_20180511154029734\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 5 jobs to complete...\n",
      "Waiting for 5 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0012_socnsLOI2_1_preGLM0_ciftiTrue_20180511155030472\n",
      "submitted sCC0027_movie_1_preGLM0_ciftiTrue_20180511155030588\n",
      "submitted sCC0027_movie_2_preGLM0_ciftiTrue_20180511155030881\n",
      "submitted sCC0027_LOI1_1_preGLM0_ciftiTrue_20180511155031109\n",
      "submitted sCC0027_LOI2_1_preGLM0_ciftiTrue_20180511155031253\n",
      "submitted sCC0027_socnsLOI1_1_preGLM0_ciftiTrue_20180511155031378\n",
      "submitted sCC0027_socnsLOI2_1_preGLM0_ciftiTrue_20180511155031485\n",
      "submitted sCC0029_movie_1_preGLM0_ciftiTrue_20180511155031592\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0029_movie_2_preGLM0_ciftiTrue_20180511160132896\n",
      "submitted sCC0029_LOI1_1_preGLM0_ciftiTrue_20180511160133184\n",
      "submitted sCC0029_LOI2_1_preGLM0_ciftiTrue_20180511160133590\n",
      "submitted sCC0029_socnsLOI1_1_preGLM0_ciftiTrue_20180511160133948\n",
      "submitted sCC0029_socnsLOI2_1_preGLM0_ciftiTrue_20180511160134094\n",
      "submitted sCC0033_movie_1_preGLM0_ciftiTrue_20180511160134238\n",
      "submitted sCC0033_movie_2_preGLM0_ciftiTrue_20180511160134509\n",
      "submitted sCC0033_LOI1_1_preGLM0_ciftiTrue_20180511160134622\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0033_LOI2_1_preGLM0_ciftiTrue_20180511161435520\n",
      "submitted sCC0033_socnsLOI1_1_preGLM0_ciftiTrue_20180511161435675\n",
      "submitted sCC0033_socnsLOI2_1_preGLM0_ciftiTrue_20180511161435796\n",
      "submitted sCC0041_movie_1_preGLM0_ciftiTrue_20180511161435943\n",
      "submitted sCC0041_LOI1_1_preGLM0_ciftiTrue_20180511161436153\n",
      "submitted sCC0041_LOI2_1_preGLM0_ciftiTrue_20180511161436302\n",
      "submitted sCC0041_socnsLOI1_1_preGLM0_ciftiTrue_20180511161436461\n",
      "submitted sCC0041_socnsLOI2_1_preGLM0_ciftiTrue_20180511161436616\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 7 jobs to complete...\n",
      "Waiting for 7 jobs to complete...\n",
      "Waiting for 7 jobs to complete...\n",
      "Waiting for 5 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0046_movie_1_preGLM0_ciftiTrue_20180511162837710\n",
      "submitted sCC0046_movie_2_preGLM0_ciftiTrue_20180511162838082\n",
      "submitted sCC0046_LOI1_1_preGLM0_ciftiTrue_20180511162838286\n",
      "submitted sCC0046_LOI2_1_preGLM0_ciftiTrue_20180511162838513\n",
      "submitted sCC0046_socnsLOI1_1_preGLM0_ciftiTrue_20180511162838642\n",
      "submitted sCC0046_socnsLOI2_1_preGLM0_ciftiTrue_20180511162838808\n",
      "submitted sCC0049_LOI1_1_preGLM0_ciftiTrue_20180511162839035\n",
      "submitted sCC0049_LOI2_1_preGLM0_ciftiTrue_20180511162839244\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0049_socnsLOI1_1_preGLM0_ciftiTrue_20180511164040151\n",
      "submitted sCC0049_socnsLOI2_1_preGLM0_ciftiTrue_20180511164040399\n",
      "submitted sCC0063_movie_1_preGLM0_ciftiTrue_20180511164040605\n",
      "submitted sCC0063_movie_2_preGLM0_ciftiTrue_20180511164041565\n",
      "submitted sCC0063_LOI1_1_preGLM0_ciftiTrue_20180511164042081\n",
      "submitted sCC0063_LOI2_1_preGLM0_ciftiTrue_20180511164042773\n",
      "submitted sCC0063_socnsLOI1_1_preGLM0_ciftiTrue_20180511164043211\n",
      "submitted sCC0063_socnsLOI2_1_preGLM0_ciftiTrue_20180511164043647\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 5 jobs to complete...\n",
      "Waiting for 5 jobs to complete...\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0068_movie_1_preGLM0_ciftiTrue_20180511165045404\n",
      "submitted sCC0068_movie_2_preGLM0_ciftiTrue_20180511165046322\n",
      "submitted sCC0068_LOI1_1_preGLM0_ciftiTrue_20180511165046861\n",
      "submitted sCC0068_LOI2_1_preGLM0_ciftiTrue_20180511165047354\n",
      "submitted sCC0068_socnsLOI1_1_preGLM0_ciftiTrue_20180511165047875\n",
      "submitted sCC0068_socnsLOI2_1_preGLM0_ciftiTrue_20180511165048423\n",
      "submitted sCC0080_movie_1_preGLM0_ciftiTrue_20180511165050557\n",
      "submitted sCC0080_movie_2_preGLM0_ciftiTrue_20180511165051281\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 6 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0080_LOI1_1_preGLM0_ciftiTrue_20180511170052412\n",
      "submitted sCC0080_LOI2_1_preGLM0_ciftiTrue_20180511170052849\n",
      "submitted sCC0080_socnsLOI1_1_preGLM0_ciftiTrue_20180511170053286\n",
      "submitted sCC0080_socnsLOI2_1_preGLM0_ciftiTrue_20180511170053782\n",
      "submitted sCC0081_movie_1_preGLM0_ciftiTrue_20180511170054790\n",
      "submitted sCC0081_movie_2_preGLM0_ciftiTrue_20180511170055625\n",
      "submitted sCC0081_LOI1_1_preGLM0_ciftiTrue_20180511170056187\n",
      "submitted sCC0081_LOI2_1_preGLM0_ciftiTrue_20180511170056988\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0081_socnsLOI1_1_preGLM0_ciftiTrue_20180511170858112\n",
      "submitted sCC0081_socnsLOI2_1_preGLM0_ciftiTrue_20180511170858563\n",
      "submitted sCC0085_movie_1_preGLM0_ciftiTrue_20180511170859499\n",
      "submitted sCC0085_movie_2_preGLM0_ciftiTrue_20180511170900380\n",
      "submitted sCC0085_LOI1_1_preGLM0_ciftiTrue_20180511170900793\n",
      "submitted sCC0085_LOI2_1_preGLM0_ciftiTrue_20180511170901253\n",
      "submitted sCC0085_socnsLOI1_1_preGLM0_ciftiTrue_20180511170901723\n",
      "submitted sCC0085_socnsLOI2_1_preGLM0_ciftiTrue_20180511170902203\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 5 jobs to complete...\n",
      "Waiting for 5 jobs to complete...\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0104_movie_1_preGLM0_ciftiTrue_20180511172005087\n",
      "submitted sCC0104_movie_2_preGLM0_ciftiTrue_20180511172005796\n",
      "submitted sCC0104_LOI1_1_preGLM0_ciftiTrue_20180511172006813\n",
      "submitted sCC0104_LOI2_1_preGLM0_ciftiTrue_20180511172007224\n",
      "submitted sCC0104_socnsLOI1_1_preGLM0_ciftiTrue_20180511172007767\n",
      "submitted sCC0104_socnsLOI2_1_preGLM0_ciftiTrue_20180511172008221\n",
      "submitted sCC0106_movie_1_preGLM0_ciftiTrue_20180511172009137\n",
      "submitted sCC0106_movie_2_preGLM0_ciftiTrue_20180511172009874\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0106_LOI1_1_preGLM0_ciftiTrue_20180511172910765\n",
      "submitted sCC0106_LOI2_1_preGLM0_ciftiTrue_20180511172911218\n",
      "submitted sCC0106_socnsLOI1_1_preGLM0_ciftiTrue_20180511172911787\n",
      "submitted sCC0106_socnsLOI2_1_preGLM0_ciftiTrue_20180511172912306\n",
      "submitted sCC0108_movie_1_preGLM0_ciftiTrue_20180511172913177\n",
      "submitted sCC0108_movie_2_preGLM0_ciftiTrue_20180511172913787\n",
      "submitted sCC0108_LOI1_1_preGLM0_ciftiTrue_20180511172914219\n",
      "submitted sCC0108_LOI2_1_preGLM0_ciftiTrue_20180511172914730\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 5 jobs to complete...\n",
      "Waiting for 5 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0108_socnsLOI1_1_preGLM0_ciftiTrue_20180511173515467\n",
      "submitted sCC0108_socnsLOI2_1_preGLM0_ciftiTrue_20180511173515876\n",
      "submitted sCC0111_movie_1_preGLM0_ciftiTrue_20180511173516746\n",
      "submitted sCC0111_movie_2_preGLM0_ciftiTrue_20180511173517358\n",
      "submitted sCC0111_LOI1_1_preGLM0_ciftiTrue_20180511173517738\n",
      "submitted sCC0111_LOI2_1_preGLM0_ciftiTrue_20180511173518197\n",
      "submitted sCC0111_socnsLOI1_1_preGLM0_ciftiTrue_20180511173518686\n",
      "submitted sCC0111_socnsLOI2_1_preGLM0_ciftiTrue_20180511173519133\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 5 jobs to complete...\n",
      "Waiting for 5 jobs to complete...\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0114_movie_1_preGLM0_ciftiTrue_20180511174620574\n",
      "submitted sCC0114_movie_2_preGLM0_ciftiTrue_20180511174621778\n",
      "submitted sCC0114_LOI1_1_preGLM0_ciftiTrue_20180511174622225\n",
      "submitted sCC0114_LOI2_1_preGLM0_ciftiTrue_20180511174622623\n",
      "submitted sCC0114_socnsLOI1_1_preGLM0_ciftiTrue_20180511174623086\n",
      "submitted sCC0114_socnsLOI2_1_preGLM0_ciftiTrue_20180511174623589\n",
      "submitted sCC0117_movie_1_preGLM0_ciftiTrue_20180511174625045\n",
      "submitted sCC0117_movie_2_preGLM0_ciftiTrue_20180511174625647\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 8 jobs to complete...\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "All done!!\n",
      "submitted sCC0117_LOI1_1_preGLM0_ciftiTrue_20180511175727567\n",
      "submitted sCC0117_LOI2_1_preGLM0_ciftiTrue_20180511175728038\n",
      "submitted sCC0117_socnsLOI1_1_preGLM0_ciftiTrue_20180511175728542\n",
      "submitted sCC0117_socnsLOI2_1_preGLM0_ciftiTrue_20180511175729135\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 4 jobs to complete...\n",
      "Waiting for 3 jobs to complete...\n",
      "Waiting for 2 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "Waiting for 1 jobs to complete...\n",
      "All done!!\n",
      "CC0003 -- movie_1 -- OK\n",
      "CC0003 -- movie_2 -- OK\n",
      "CC0006 -- movie_1 -- OK\n",
      "CC0006 -- movie_2 -- OK\n",
      "CC0006 -- LOI2_1 -- OK\n",
      "CC0006 -- socnsLOI1_1 -- OK\n",
      "CC0006 -- socnsLOI2_1 -- OK\n",
      "CC0007 -- movie_1 -- OK\n",
      "CC0007 -- movie_2 -- OK\n",
      "CC0007 -- LOI1_1 -- OK\n",
      "CC0007 -- LOI2_1 -- OK\n",
      "CC0007 -- socnsLOI1_1 -- OK\n",
      "CC0007 -- socnsLOI2_1 -- OK\n",
      "CC0008 -- movie_1 -- OK\n",
      "CC0008 -- movie_2 -- OK\n",
      "CC0008 -- LOI1_1 -- OK\n",
      "CC0008 -- LOI2_1 -- OK\n",
      "CC0008 -- socnsLOI1_1 -- OK\n",
      "CC0008 -- socnsLOI2_1 -- OK\n",
      "CC0012 -- movie_1 -- OK\n",
      "CC0012 -- movie_2 -- OK\n",
      "CC0012 -- LOI1_1 -- OK\n",
      "CC0012 -- LOI2_1 -- OK\n",
      "CC0012 -- socnsLOI1_1 -- OK\n",
      "CC0012 -- socnsLOI2_1 -- OK\n",
      "CC0027 -- movie_1 -- OK\n",
      "CC0027 -- movie_2 -- OK\n",
      "CC0027 -- LOI1_1 -- OK\n",
      "CC0027 -- LOI2_1 -- OK\n",
      "CC0027 -- socnsLOI1_1 -- OK\n",
      "CC0027 -- socnsLOI2_1 -- OK\n",
      "CC0029 -- movie_1 -- OK\n",
      "CC0029 -- movie_2 -- OK\n",
      "CC0029 -- LOI1_1 -- OK\n",
      "CC0029 -- LOI2_1 -- OK\n",
      "CC0029 -- socnsLOI1_1 -- OK\n",
      "CC0029 -- socnsLOI2_1 -- OK\n",
      "CC0033 -- movie_1 -- OK\n",
      "CC0033 -- movie_2 -- OK\n",
      "CC0033 -- LOI1_1 -- OK\n",
      "CC0033 -- LOI2_1 -- OK\n",
      "CC0033 -- socnsLOI1_1 -- OK\n",
      "CC0033 -- socnsLOI2_1 -- OK\n",
      "CC0041 -- movie_1 -- OK\n",
      "CC0041 -- LOI1_1 -- OK\n",
      "CC0041 -- LOI2_1 -- OK\n",
      "CC0041 -- socnsLOI1_1 -- OK\n",
      "CC0041 -- socnsLOI2_1 -- OK\n",
      "CC0046 -- movie_1 -- OK\n",
      "CC0046 -- movie_2 -- OK\n",
      "CC0046 -- LOI1_1 -- OK\n",
      "CC0046 -- LOI2_1 -- OK\n",
      "CC0046 -- socnsLOI1_1 -- OK\n",
      "CC0046 -- socnsLOI2_1 -- OK\n",
      "CC0049 -- LOI1_1 -- OK\n",
      "CC0049 -- LOI2_1 -- OK\n",
      "CC0049 -- socnsLOI1_1 -- OK\n",
      "CC0049 -- socnsLOI2_1 -- OK\n",
      "CC0063 -- movie_1 -- OK\n",
      "CC0063 -- movie_2 -- OK\n",
      "CC0063 -- LOI1_1 -- OK\n",
      "CC0063 -- LOI2_1 -- OK\n",
      "CC0063 -- socnsLOI1_1 -- OK\n",
      "CC0063 -- socnsLOI2_1 -- OK\n",
      "CC0068 -- movie_1 -- OK\n",
      "CC0068 -- movie_2 -- OK\n",
      "CC0068 -- LOI1_1 -- OK\n",
      "CC0068 -- LOI2_1 -- OK\n",
      "CC0068 -- socnsLOI1_1 -- OK\n",
      "CC0068 -- socnsLOI2_1 -- OK\n",
      "CC0080 -- movie_1 -- OK\n",
      "CC0080 -- movie_2 -- OK\n",
      "CC0080 -- LOI1_1 -- OK\n",
      "CC0080 -- LOI2_1 -- OK\n",
      "CC0080 -- socnsLOI1_1 -- OK\n",
      "CC0080 -- socnsLOI2_1 -- OK\n",
      "CC0081 -- movie_1 -- OK\n",
      "CC0081 -- movie_2 -- OK\n",
      "CC0081 -- LOI1_1 -- OK\n",
      "CC0081 -- LOI2_1 -- OK\n",
      "CC0081 -- socnsLOI1_1 -- OK\n",
      "CC0081 -- socnsLOI2_1 -- OK\n",
      "CC0085 -- movie_1 -- OK\n",
      "CC0085 -- movie_2 -- OK\n",
      "CC0085 -- LOI1_1 -- OK\n",
      "CC0085 -- LOI2_1 -- OK\n",
      "CC0085 -- socnsLOI1_1 -- OK\n",
      "CC0085 -- socnsLOI2_1 -- OK\n",
      "CC0104 -- movie_1 -- OK\n",
      "CC0104 -- movie_2 -- OK\n",
      "CC0104 -- LOI1_1 -- OK\n",
      "CC0104 -- LOI2_1 -- OK\n",
      "CC0104 -- socnsLOI1_1 -- OK\n",
      "CC0104 -- socnsLOI2_1 -- OK\n",
      "CC0106 -- movie_1 -- OK\n",
      "CC0106 -- movie_2 -- OK\n",
      "CC0106 -- LOI1_1 -- OK\n",
      "CC0106 -- LOI2_1 -- OK\n",
      "CC0106 -- socnsLOI1_1 -- OK\n",
      "CC0106 -- socnsLOI2_1 -- OK\n",
      "CC0108 -- movie_1 -- OK\n",
      "CC0108 -- movie_2 -- OK\n",
      "CC0108 -- LOI1_1 -- OK\n",
      "CC0108 -- LOI2_1 -- OK\n",
      "CC0108 -- socnsLOI1_1 -- OK\n",
      "CC0108 -- socnsLOI2_1 -- OK\n",
      "CC0111 -- movie_1 -- OK\n",
      "CC0111 -- movie_2 -- OK\n",
      "CC0111 -- LOI1_1 -- OK\n",
      "CC0111 -- LOI2_1 -- OK\n",
      "CC0111 -- socnsLOI1_1 -- OK\n",
      "CC0111 -- socnsLOI2_1 -- OK\n",
      "CC0114 -- movie_1 -- OK\n",
      "CC0114 -- movie_2 -- OK\n",
      "CC0114 -- LOI1_1 -- OK\n",
      "CC0114 -- LOI2_1 -- OK\n",
      "CC0114 -- socnsLOI1_1 -- OK\n",
      "CC0114 -- socnsLOI2_1 -- OK\n",
      "CC0117 -- movie_1 -- OK\n",
      "CC0117 -- movie_2 -- OK\n",
      "CC0117 -- LOI1_1 -- OK\n",
      "CC0117 -- LOI2_1 -- OK\n",
      "CC0117 -- socnsLOI1_1 -- OK\n",
      "CC0117 -- socnsLOI2_1 -- OK\n"
     ]
    }
   ],
   "source": [
    "config.overwrite               = False\n",
    "config.Operations              = config.operationDict[config.pipelineName]\n",
    "\n",
    "if config.pipelineName in ['SiegelA','SiegelB']:\n",
    "    config.useFIX              = True\n",
    "else:\n",
    "    config.useFIX              = False\n",
    "\n",
    "returnhere = os.getcwd()\n",
    "\n",
    "# do the work\n",
    "config.joblist = list()\n",
    "iSub    = 0\n",
    "for subject in subjects:\n",
    "    config.subject = str(subject)\n",
    "    iRun = 0\n",
    "    for config.fmriRun in fmriRuns:\n",
    "        runPipelinePar(launchSubproc=launchSubproc)\n",
    "        iRun=iRun+1\n",
    "        if len(config.joblist)>=8:\n",
    "            # wait until all tasks are done\n",
    "            checkProgress(verbose=True)\n",
    "            config.joblist = list()\n",
    "    iSub = iSub + 1\n",
    "\n",
    "if len(config.joblist)>0:\n",
    "    checkProgress(verbose=True) \n",
    "    \n",
    "# make symlinks\n",
    "keepSub = np.zeros((len(subjects),len(fmriRuns)),dtype=np.bool_)\n",
    "iSub    = 0\n",
    "for subject in subjects:\n",
    "    config.subject = str(subject)\n",
    "    iRun = 0\n",
    "    for config.fmriRun in fmriRuns:\n",
    "        keepSub[iSub,iRun] = runPipelinePar(launchSubproc=False)\n",
    "        if keepSub[iSub,iRun]:\n",
    "            os.chdir(op.dirname(buildpath()))\n",
    "            if op.isdir(buildpath()+'_'+config.pipelineName):\n",
    "                remove(buildpath()+'_'+config.pipelineName)\n",
    "            os.symlink(op.basename(buildpath()),\n",
    "                op.basename(buildpath())+'_'+config.pipelineName)\n",
    "            if op.exists(op.join(buildpath(),config.fmriRun+'_'+config.pipelineName+config.ext)):\n",
    "                remove(op.join(buildpath(),config.fmriRun+'_'+config.pipelineName+config.ext))\n",
    "            if op.exists(op.join(buildpath(),config.fmriRun+'_'+config.pipelineName+'_Atlas'+config.ext)):\n",
    "                remove(op.join(buildpath(),config.fmriRun+'_'+config.pipelineName+'_Atlas'+config.ext))\n",
    "            os.chdir(buildpath())\n",
    "            os.symlink(op.basename(config.fmriFile_dn),\n",
    "                  config.fmriRun+'_'+config.pipelineName+'_Atlas'+config.ext)\n",
    "            print '{} -- {} -- OK'.format(config.subject,config.fmriRun)\n",
    "            os.chdir(returnhere)\n",
    "        iRun=iRun+1\n",
    "    iSub = iSub + 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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