pipeline_1a_functionalsessions_raw2bids.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This script converts dicoms of the functional sessions ('ses-se', 'ses-me') to Nifti in bids-format"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import nibabel as nib\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "import json\n",
    "from glob import glob\n",
    "from pprint import pprint\n",
    "import matplotlib.pyplot as plt\n",
    "import seaborn as sns\n",
    "import re\n",
    "#%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# global options/settings\n",
    "ext = '.nii'\n",
    "root_raw_data = '/home/stevenm/MultiEchoEPISeq/data/raw/dicom'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Dicom to nifti conversion"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 110,
   "metadata": {},
   "outputs": [],
   "source": [
    "dcm2nii_dict = {\n",
    "    'sub-01': {\n",
    "        'ses-se': 'bd0499ff-e709a583-4e1d5117-f7108599-75f20412.zip',\n",
    "        'ses-me': 'f4ca606c-44fa5000-cd822d6e-f4afaec5-347723d8.zip'\n",
    "    },\n",
    "    'sub-02': {\n",
    "        'ses-me': 'aa992687-6be019be-f5573e8f-79174cd0-17bfe594.zip',\n",
    "        'ses-se': '6113a245-de260a27-4e914f58-1e86e635-00fd7938.zip'\n",
    "    },\n",
    "    'sub-03': {\n",
    "        'ses-se': 'e8d86fc2-d960e9aa-c21a86ca-1527352d-e4f7779a.zip',\n",
    "        'ses-me': '7b68e417-d3c63cec-9aeabf5c-4ac1ecbe-b4f2cd53.zip'\n",
    "    },\n",
    "    'sub-04': {\n",
    "        'ses-me': '6994f153-caf09c0a-155a6e7d-bba5024a-1169c647.zip',\n",
    "        'ses-se': '7dcd5ff5-068d24b0-d8e5938e-baf89605-b50777d3.zip'\n",
    "    },\n",
    "    'sub-05': {\n",
    "        'ses-se': '7a931048-ebba8ca7-2dcb5706-fb5ab19b-8ffcdd2f.zip',\n",
    "        'ses-me': '5a305d22-e4c90ca7-43b6bf58-4df4d956-a3c7898e.zip'\n",
    "    },\n",
    "    'sub-06': {\n",
    "        'ses-me': 'f3871193-d66be461-753f80f1-17358447-a366f18f.zip',\n",
    "        'ses-se': '85f77949-7e77a5e6-89d92727-8f8cf99b-6c42b18a.zip'\n",
    "    },\n",
    "    'sub-07': {\n",
    "        'ses-se': '60a39eec-8a8904db-c51af47b-0ce64312-ce9a65f1.zip',\n",
    "        'ses-me': '34cc68bb-f862cff0-641c6c79-d4b40211-a647420f.zip'\n",
    "    },\n",
    "    'sub-08': {\n",
    "        'ses-me': '00fab4d5-76881a0f-29ae2073-9ae3e64d-97a2b83f.zip',\n",
    "        'ses-se': '661928f3-b6012b3e-5d26d11b-3a8bdccb-2b6aedb3.zip'\n",
    "    },\n",
    "    'sub-09': {\n",
    "        'ses-se': 'c7f6968f-c1f83abc-c9e3572f-bc85146f-9604f8b1.zip',\n",
    "        'ses-me': '64f7bc2a-f0327997-d29ed8a0-870dc7d4-dac3b553.zip'\n",
    "    },\n",
    "    'sub-10': {\n",
    "        'ses-me': '894335be-6d4c927f-1b5b3c25-a94489c0-6cda18ec.zip',\n",
    "        'ses-se': '542d7eab-bc4947a7-ac2ba2c3-0bfb6a27-bcb07700.zip'\n",
    "    },\n",
    "    'sub-11': {\n",
    "        'ses-se': '80f57752-8f671d5b-40fdfde7-cad60037-2322692c.zip',\n",
    "        'ses-me': '31bd7265-01496729-aedc2355-4e69cc03-3bd5600c.zip'\n",
    "    },\n",
    "    'sub-12': {\n",
    "        'ses-me': '8a970dad-ac1217ad-5fca9e7e-b947cdf3-8e119b7c.zip',\n",
    "        'ses-se': 'e187c97e-68ecca03-7b19801d-bde41eaf-434fcf5d.zip'\n",
    "    },\n",
    "    'sub-13': {\n",
    "        'ses-se': '5a217187-3550aaa7-fc2e459c-7f9a13f5-bcc99461.zip',\n",
    "        'ses-me': 'aa6bc799-4c08de45-28267adb-98f5c6f6-5e2b4299.zip'\n",
    "    },\n",
    "    'sub-14': {\n",
    "        'ses-me': '9d1f88fd-b6e119d3-61859c3c-b7b0d49c-4eea3e59.zip',\n",
    "        'ses-se': '78280164-f8e44d4d-6c1d17fc-75470488-9bf9c092.zip'\n",
    "    },\n",
    "    'sub-15': {\n",
    "        'ses-se': 'de00c317-c8015163-6539667d-4e18a7c0-57591eec.zip',\n",
    "        'ses-me': '15484.08'  # this original zip file was corrupted and replaced by a new download in a slightly different format\n",
    "    },\n",
    "    'sub-16': {\n",
    "        'ses-me': '53dad91d-567101c3-f64ac66b-f1362639-4278144a.zip',\n",
    "        'ses-se': '894ca696-00b7f86c-9e74dbed-9982f17b-872a13b5.zip'\n",
    "    },\n",
    "    'sub-17': {\n",
    "        'ses-se': '4edc6117-509509d0-9fb174ed-0fb2120d-e1fde59d.zip',\n",
    "        'ses-me': '9448464d-3cf9f4f4-7922dd68-ed2047a6-943e54bd.zip'\n",
    "    },\n",
    "    'sub-18': {\n",
    "        'ses-me': '1f88a319-802adc86-f2154ca5-3f4b9d76-62056c19.zip',\n",
    "        'ses-se': 'bea9deb0-2622a572-c0630182-ab3d9d0d-954536c0.zip'\n",
    "    }\n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. Dicom to Nifti"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 111,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['unzip /home/stevenm/MultiEchoEPISeq/data/raw/dicom/5a217187-3550aaa7-fc2e459c-7f9a13f5-bcc99461.zip -d /home/stevenm/MultiEchoEPISeq/data/raw/dicom/tmp_0 && dcm2niix -6 -b y -i y -f %s_%d_echo-%e -o /home/stevenm/MultiEchoEPISeq/data/raw/nifti/sub-13/ses-se /home/stevenm/MultiEchoEPISeq/data/raw/dicom/tmp_0 && rm -r /home/stevenm/MultiEchoEPISeq/data/raw/dicom/tmp_0']"
      ]
     },
     "execution_count": 111,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#\n",
    "\n",
    "from_files = []\n",
    "to_files = []\n",
    "\n",
    "for sub_idx, session_dict in dcm2nii_dict.items():\n",
    "    for session_name, raw_dir in session_dict.items():\n",
    "        if not (sub_idx == 'sub-13' and session_name=='ses-se'):\n",
    "            continue\n",
    "        nii_data_location = './data/raw/nifti/%s/%s' %(sub_idx, session_name)\n",
    "        \n",
    "        from_files.append(os.path.join(root_raw_data, raw_dir))\n",
    "        to_files.append(os.path.join(nii_data_location, '%s_%s' %(sub_idx, session_name)))\n",
    "        \n",
    "# check for existence of output files\n",
    "to_process = []\n",
    "for from_fn, to_fn in zip(from_files, to_files):\n",
    "    to_process.append([from_fn, to_fn])\n",
    "\n",
    "cmds = []\n",
    "for i, fns in enumerate(to_process):\n",
    "    out_name = os.path.basename(fns[1])\n",
    "    out_dir = os.path.abspath(os.path.dirname(fns[1]))\n",
    "    tmp_dir = os.path.dirname(fns[0]) + '/tmp_' + str(i)\n",
    "    if not os.path.exists(out_dir):\n",
    "        os.makedirs(out_dir)\n",
    "    \n",
    "    if fns[0].endswith('.zip'):\n",
    "        #unzip to tmp folder, convert to nifti, remove unzipped tmp folder (for some reason dcm2niix on Linux doesnt accept zip files)\n",
    "        cmds.append('unzip {} -d {} && dcm2niix -6 -b y -i y -f %s_%d_echo-%e -o {} {} && rm -r {}'.format(fns[0],\n",
    "                                                                                                        tmp_dir,\n",
    "                                                                                                        out_dir, \n",
    "                                                                                                        tmp_dir,\n",
    "                                                                                                        tmp_dir))\n",
    "    else:\n",
    "        cmds.append(\"unzip '{}/*.zip' -d {} && dcm2niix -6 -b y -i y -f %s_%d_echo-%e -o {} {} && rm -r {}\".format(fns[0],\n",
    "                                                                                                                tmp_dir,\n",
    "                                                                                                                out_dir, \n",
    "                                                                                                                tmp_dir,\n",
    "                                                                                                                tmp_dir))\n",
    "cmds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 112,
   "metadata": {},
   "outputs": [],
   "source": [
    "def run_cmd(x):\n",
    "    os.system(x)\n",
    "\n",
    "from multiprocessing import Pool\n",
    "\n",
    "with Pool(10) as p:\n",
    "    p.map(run_cmd, cmds)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 2. Nifti to BIDS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 113,
   "metadata": {},
   "outputs": [],
   "source": [
    "nii2bids_dict = {\n",
    "    'sub-01': { \n",
    "         'ses-se': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S1s1-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '11_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '12_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '9_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '10_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '5_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '8_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '6_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '6_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '7_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "        'ses-me': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S1s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "    },\n",
    "    'sub-02': { \n",
    "         'ses-me': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S2s1-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '9_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '10_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '11_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "        'ses-se': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S2s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "            'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "            'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        }\n",
    "    },\n",
    "    'sub-03': { \n",
    "         'ses-se': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S3s1-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "        'ses-me': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S3s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '9_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '10_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '11_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "    },\n",
    "    'sub-04': { \n",
    "         'ses-me': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S4s1-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '9_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '10_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '11_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "         'ses-se': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S4s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '9_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '10_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '11_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "    },\n",
    "    'sub-05': { \n",
    "         'ses-se': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S5s1-stop_fmri.log',\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '8_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "         'ses-me': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S5s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "    },\n",
    "    'sub-06': {\n",
    "         'ses-me': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S6s1-stop_fmri.log',\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '5_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '6_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '10_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '7_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '7_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '8_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "         'ses-se': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S6s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '11_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '12_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '9_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '10_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '5_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '8_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '6_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '6_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '7_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "    },\n",
    "    'sub-07': {\n",
    "        'ses-se': {\n",
    "             'anat': {\n",
    "                 'T1map': '9_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '10_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '11_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        },\n",
    "         'ses-me': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S7s1-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "    },\n",
    "    'sub-08': {\n",
    "         'ses-me': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S8s1-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "        'ses-se': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S8s2-stop_fmri.log',\n",
    "#              'anat': {\n",
    "#                  'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "#                  'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "#                  'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "#                  'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        }\n",
    "\n",
    "    },\n",
    "    'sub-09': {\n",
    "        'ses-se': {\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        },\n",
    "         'ses-me': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S9s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "    },\n",
    "    'sub-10': {\n",
    "         'ses-me': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S10s1-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "        'ses-se': {\n",
    "             'behavioral_log_file': './data/raw/behavior/S10s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '9_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '10_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '11_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        },\n",
    "    },\n",
    "    'sub-11': {\n",
    "        'ses-se': {\n",
    "             'anat': {\n",
    "                 'T1map': '9_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '10_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '11_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        },\n",
    "         'ses-me': {\n",
    "#             'behavioral_log_file': './data/raw/behavior/S11s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "    },\n",
    "    'sub-12': {\n",
    "#          'ses-me': {\n",
    "#               # consider this run a failure, unfortunately\n",
    "#              'behavioral_log_file': './data/raw/behavior/S10s1-stop_fmri.log',\n",
    "#              'anat': {\n",
    "#                  'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "#                  'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "#                  'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "#                  'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "#              'func': {\n",
    "#                  'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "#                  'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "#                  'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "#              'fmap': {\n",
    "#                  'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "#                  'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "#                  'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "#              },\n",
    "        'ses-se': {\n",
    "#             'behavioral_log_file': './data/raw/behavior/S10s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        },\n",
    "    },\n",
    "    'sub-13': {\n",
    "        'ses-se': {\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        },\n",
    "         'ses-me': {\n",
    "#             'behavioral_log_file': './data/raw/behavior/S11s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "         },\n",
    "    },\n",
    "    'sub-14': {\n",
    "         'ses-me': {\n",
    "#              'behavioral_log_file': './data/raw/behavior/S10s1-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '9_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '10_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '11_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "        'ses-se': {\n",
    "#             'behavioral_log_file': './data/raw/behavior/S10s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        },\n",
    "    },\n",
    "    'sub-15': {\n",
    "        'ses-se': {\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        },\n",
    "         'ses-me': {\n",
    "#             'behavioral_log_file': './data/raw/behavior/S11s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "    },\n",
    "    'sub-16': {\n",
    "         'ses-me': {\n",
    "#             'behavioral_log_file': './data/raw/behavior/S10s1-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "        'ses-se': {\n",
    "#             'behavioral_log_file': './data/raw/behavior/S10s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '9_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '10_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '11_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        },\n",
    "    },\n",
    "    'sub-17': {\n",
    "        'ses-se': {\n",
    "             'anat': {\n",
    "                 'T1map': '9_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '10_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '11_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        },\n",
    "         'ses-me': {\n",
    "#             'behavioral_log_file': './data/raw/behavior/S11s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '9_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '10_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '11_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "    },\n",
    "    'sub-18': {\n",
    "         'ses-me': {\n",
    "#              'behavioral_log_file': './data/raw/behavior/S10s1-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_echo-1_bold': '3_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-2_echo-1_bold': '4_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1',\n",
    "                 'task-stop_run-3_echo-1_bold': '7_MultiEcho_2D_TR3000_TE9p66-24p87-40p08_1p6_70sli_bFOV_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "             },\n",
    "        'ses-se': {\n",
    "#             'behavioral_log_file': './data/raw/behavior/S10s2-stop_fmri.log',\n",
    "             'anat': {\n",
    "                 'T1map': '10_mp2rage_whole-brain_0p7_T1_Images_echo-1',\n",
    "                 'T1w': '11_mp2rage_whole-brain_0p7_UNI_Images_echo-1',\n",
    "                 'inv-1_MPRAGE': '8_mp2rage_whole-brain_0p7_INV1_echo-1',\n",
    "                 'inv-2_MPRAGE': '9_mp2rage_whole-brain_0p7_INV2_echo-1'},\n",
    "             'func': {\n",
    "                 'task-stop_run-1_bold': '3_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-2_bold': '4_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1',\n",
    "                 'task-stop_run-3_bold': '7_SingleEcho_2D_TR3000_TE14p0_1p6_70sl_echo-1'}, \n",
    "             'fmap': {\n",
    "                 'magnitude1': '5_fieldmap56_DeltaTE1p02ms_echo-1',\n",
    "                 'magnitude2': '5_fieldmap56_DeltaTE1p02ms_echo-2',\n",
    "                 'phasediff': '6_fieldmap56_DeltaTE1p02ms_echo-2_ph'}\n",
    "        },\n",
    "    }\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "#!ls ./data/raw/nifti/sub-06/ses-me/\n",
    "# ./data/raw/nifti/sub-02/ses-me/\n",
    "# 10_mp2rage_whole-brain_0p7_T1_Images_echo-1.nii.gz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 121,
   "metadata": {},
   "outputs": [],
   "source": [
    "root_dir = './data/raw/nifti'\n",
    "bids_dir = './data/raw/bids'\n",
    "\n",
    "from_files = []\n",
    "to_files = []\n",
    "\n",
    "\n",
    "for sub_idx, session_dict in nii2bids_dict.items():\n",
    "    for session_name, session_subdict in session_dict.items():\n",
    "        if not (sub_idx == 'sub-13' and session_name=='ses-se'):\n",
    "            continue\n",
    "        nii_data_location = root_dir + '/%s/%s' %(sub_idx, session_name)\n",
    "        bids_data_location = bids_dir + '/%s/%s' %(sub_idx, session_name)\n",
    "        for data_type in ['anat', 'func', 'fmap']:\n",
    "            if not data_type in session_subdict.keys():\n",
    "                continue\n",
    "            \n",
    "            for to_name, from_name in session_subdict[data_type].items():\n",
    "                from_files.append(os.path.join(nii_data_location, from_name))\n",
    "                to_files.append(os.path.join(bids_data_location, data_type, \n",
    "                                             '%s_%s_%s' %(sub_idx, session_name, to_name)))\n",
    "                if session_name == 'ses-me' and 'MultiEcho' in from_name:\n",
    "                    from_files.append(os.path.join(nii_data_location, from_name.replace('_echo-1', '_echo-2')))\n",
    "                    from_files.append(os.path.join(nii_data_location, from_name.replace('_echo-1', '_echo-3')))\n",
    "                    to_files.append(bids_data_location + '/' + data_type + '/%s_%s_%s' %(sub_idx, session_name, to_name.replace('echo-1', 'echo-2')))\n",
    "                    to_files.append(bids_data_location + '/' + data_type + '/%s_%s_%s' %(sub_idx, session_name, to_name.replace('echo-1', 'echo-3')))\n",
    "\n",
    "# check if to_files already exist\n",
    "from_name_final = []\n",
    "to_name_final = []\n",
    "for from_name, to_name in zip(from_files, to_files):\n",
    "#     if 'echo-' in to_name:\n",
    "#         if os.path.exists(to_name.replace('_echo-1', '').replace('_echo-2', '').replace('_echo-3', '') + '.nii.gz'):\n",
    "#             continue\n",
    "#     if os.path.exists(to_name + '.nii.gz'):\n",
    "#         continue\n",
    "    from_name_final.append(from_name)\n",
    "    to_name_final.append(to_name)\n",
    "\n",
    "# Rename everything\n",
    "for from_name, to_name in zip(from_name_final, to_name_final):\n",
    "    # check if dir exists\n",
    "    if not os.path.exists(os.path.dirname(to_name)):\n",
    "        os.makedirs(os.path.dirname(to_name))\n",
    "    \n",
    "    if not os.path.exists(from_name + ext):\n",
    "        print('Could not move %s; already moved?' %from_name)\n",
    "    else:\n",
    "        os.rename(from_name + ext, to_name + ext)\n",
    "        os.rename(from_name + '.json', to_name + '.json')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 120,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 8\r\n",
      "drwxr-xr-x 2 marcus users 4096 nov 22 12:25 .\r\n",
      "drwxr-xr-x 5 marcus users 4096 nov 22 12:25 ..\r\n"
     ]
    }
   ],
   "source": [
    "!ls -la ./data/raw/bids/sub-13/ses-se/anat"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['./data/raw/bids/sub-13/ses-se/anat/sub-13_ses-se_T1map',\n",
       " './data/raw/bids/sub-13/ses-se/anat/sub-13_ses-se_T1w',\n",
       " './data/raw/bids/sub-13/ses-se/anat/sub-13_ses-se_inv-1_MPRAGE',\n",
       " './data/raw/bids/sub-13/ses-se/anat/sub-13_ses-se_inv-2_MPRAGE',\n",
       " './data/raw/bids/sub-13/ses-se/func/sub-13_ses-se_task-stop_run-1_bold',\n",
       " './data/raw/bids/sub-13/ses-se/func/sub-13_ses-se_task-stop_run-2_bold',\n",
       " './data/raw/bids/sub-13/ses-se/func/sub-13_ses-se_task-stop_run-3_bold',\n",
       " './data/raw/bids/sub-13/ses-se/fmap/sub-13_ses-se_magnitude1',\n",
       " './data/raw/bids/sub-13/ses-se/fmap/sub-13_ses-se_magnitude2',\n",
       " './data/raw/bids/sub-13/ses-se/fmap/sub-13_ses-se_phasediff']"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "to_name_final"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 122,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "import os\n",
    "\n",
    "def list_files(startpath):\n",
    "    for root, dirs, files in os.walk(startpath):\n",
    "        level = root.replace(startpath, '').count(os.sep)\n",
    "        indent = ' ' * 4 * (level)\n",
    "        print('{}{}/'.format(indent, os.path.basename(root)))\n",
    "        subindent = ' ' * 4 * (level + 1)\n",
    "        for f in files:\n",
    "            print('{}{}'.format(subindent, f))\n",
    "# list_files('./data/raw/bids')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### Add metadata to json files\n",
    "For T1map, T1w (MP2RAGE derivatives), for functional scans, and for the fieldmap (phasediff should contain both echotimes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('./data/raw/bids/sub-01/ses-me/fmap/sub-01_ses-me_phasediff.json', 'r') as f:\n",
    "    d = json.load(f)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'Modality': 'MR',\n",
       " 'MagneticFieldStrength': 6.98,\n",
       " 'Manufacturer': 'Siemens',\n",
       " 'ManufacturersModelName': 'Investigational_Device_7T',\n",
       " 'InstitutionName': 'MPI_Leipzig',\n",
       " 'InstitutionalDepartmentName': 'Department',\n",
       " 'InstitutionAddress': 'Stephanstrasse_1a_Leipzig-FCAF96-_Leipzig_DE_04103',\n",
       " 'DeviceSerialNumber': '18919',\n",
       " 'StationName': 'SEPTEMSYS',\n",
       " 'PatientPosition': 'HFS',\n",
       " 'ProcedureStepDescription': 'TA_VB17_FATAG1',\n",
       " 'SoftwareVersions': 'syngo_MR_B17',\n",
       " 'MRAcquisitionType': '2D',\n",
       " 'SeriesDescription': 'fieldmap56_DeltaTE1p02ms',\n",
       " 'ProtocolName': 'fieldmap56_DeltaTE1p02ms',\n",
       " 'ScanningSequence': 'GR',\n",
       " 'SequenceVariant': 'SP',\n",
       " 'SequenceName': '_fm2d2r',\n",
       " 'ImageType': ['ORIGINAL', 'PRIMARY', 'P', 'ND'],\n",
       " 'SeriesNumber': 6,\n",
       " 'AcquisitionTime': '08:58:10.132500',\n",
       " 'AcquisitionNumber': 1,\n",
       " 'SliceThickness': 3.2,\n",
       " 'SpacingBetweenSlices': 3.2,\n",
       " 'SAR': 0.0520705,\n",
       " 'EchoNumber': 2,\n",
       " 'EchoTime': 0.00702,\n",
       " 'RepetitionTime': 1.5,\n",
       " 'FlipAngle': 72,\n",
       " 'PartialFourier': 1,\n",
       " 'BaseResolution': 120,\n",
       " 'ShimSetting': [136, 312, 891, 657, -65, -296, 70, -44],\n",
       " 'TxRefAmp': 222.227,\n",
       " 'PhaseResolution': 1,\n",
       " 'ReceiveCoilName': '32Ch_Head_7T',\n",
       " 'PulseSequenceDetails': '%SiemensSeq%_gre_field_mapping',\n",
       " 'PercentPhaseFOV': 100,\n",
       " 'PhaseEncodingSteps': 120,\n",
       " 'AcquisitionMatrixPE': 120,\n",
       " 'ReconMatrixPE': 120,\n",
       " 'PixelBandwidth': 260,\n",
       " 'DwellTime': 1.6e-05,\n",
       " 'PhaseEncodingDirection': 'j-',\n",
       " 'ImageOrientationPatientDICOM': [0.999173,\n",
       "  -0.0383709,\n",
       "  0.0134587,\n",
       "  0.040655,\n",
       "  0.949164,\n",
       "  -0.312146],\n",
       " 'InPlanePhaseEncodingDirectionDICOM': 'COL',\n",
       " 'ConversionSoftware': 'dcm2niix',\n",
       " 'ConversionSoftwareVersion': 'v1.0.20180918  GCC5.4.0',\n",
       " 'EchoTime1': 0.006,\n",
       " 'EchoTime2': 0.00702,\n",
       " 'IntendedFor': ['ses-me/func/sub-01_ses-me_task-stop_run-1_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-2_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-3_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-1_echo-1_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-1_echo-2_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-1_echo-3_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-2_echo-1_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-2_echo-2_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-2_echo-3_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-3_echo-1_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-3_echo-2_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-3_echo-3_bold.nii']}"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "d"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "bids_root = './data/raw/bids'\n",
    "\n",
    "T1map_jsons = glob(os.path.join(bids_root, '*', '*', '*', '*_T1map.json'))\n",
    "for T1map_json in T1map_jsons:\n",
    "    inv_1 = os.path.basename(T1map_json).replace('_T1map.json', '_inv-1_MPRAGE' + ext)\n",
    "    inv_2 = os.path.basename(T1map_json).replace('_T1map.json', '_inv-2_MPRAGE' + ext)\n",
    "\n",
    "    json_dict_t1map =  {\n",
    "        \"BasedOn\": [inv_1, inv_2],\n",
    "        \"EstimationMethod\":\"Marques et al., 2013\"\n",
    "    }\n",
    "    \n",
    "    # save this dict for both the T1map and the T1w images (these dicts are the same)\n",
    "    with open(T1map_json, 'w') as f:\n",
    "        json.dump(json_dict_t1map, f)\n",
    "    with open(T1map_json.replace('T1map', 'T1w'), 'w') as f:\n",
    "        json.dump(json_dict_t1map, f)\n",
    "\n",
    "    # TO DO: get excitation repetition time, inversion repetition time, flip angles    \n",
    "    \n",
    "# Add task description to functional jsons\n",
    "func_jsons = glob(os.path.join(bids_root, '*', '*', '*', '*_bold.json'))\n",
    "for func_json in func_jsons:\n",
    "    with open(func_json, 'r') as f:\n",
    "        this_json = json.load(f)\n",
    "    this_json['TaskName'] = 'Stop signal task'\n",
    "    this_json['CogAtlasID'] = 'tsk_4a57abb949e1a'\n",
    "    \n",
    "    with open(func_json, 'w') as f:\n",
    "        json.dump(this_json, f)\n",
    "        \n",
    "fmap_jsons = glob(os.path.join(bids_root, '*/*/*/*_phasediff.json'))\n",
    "for fmap_json in fmap_jsons:\n",
    "    with open(fmap_json, 'r') as f:\n",
    "        this_json = json.load(f)\n",
    "        \n",
    "    this_json['EchoTime1'] = 0.006  # from the magnitude1 json\n",
    "    this_json['EchoTime2'] = 0.00702 # from the magnitude2 json\n",
    "    regx = re.compile('.*sub-(?P<sub>\\d+)_ses-(?P<ses>[a-z]+)_*')\n",
    "    regx_dict = regx.match(fmap_json).groupdict()\n",
    "    if regx_dict['ses'] == 'se':\n",
    "        this_json['IntendedFor'] = [\"ses-%s/func/sub-%s_ses-%s_task-stop_run-%d_bold%s\" %(regx_dict['ses'], regx_dict['sub'], regx_dict['ses'], x, ext) for x in [1,2,3]]\n",
    "    else:\n",
    "#        this_json['IntendedFor'] = [\"ses-%s/func/sub-%s_ses-%s_task-stop_run-%d_bold%s\" %(regx_dict['ses'], regx_dict['sub'], regx_dict['ses'], x, ext) for x in [1,2,3]]\n",
    "        this_json['IntendedFor'] = [\"ses-%s/func/sub-%s_ses-%s_task-stop_run-%d_echo-%d_bold%s\" %(regx_dict['ses'], regx_dict['sub'], regx_dict['ses'], x, y, ext) for x in [1,2,3] for y in [1,2,3]]\n",
    "    \n",
    "    with open(fmap_json, 'w') as f:\n",
    "        json.dump(this_json, f)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'Modality': 'MR',\n",
       " 'MagneticFieldStrength': 6.98,\n",
       " 'Manufacturer': 'Siemens',\n",
       " 'ManufacturersModelName': 'Investigational_Device_7T',\n",
       " 'InstitutionName': 'MPI_Leipzig',\n",
       " 'InstitutionalDepartmentName': 'Department',\n",
       " 'InstitutionAddress': 'Stephanstrasse_1a_Leipzig-FCAF96-_Leipzig_DE_04103',\n",
       " 'DeviceSerialNumber': '18919',\n",
       " 'StationName': 'SEPTEMSYS',\n",
       " 'PatientPosition': 'HFS',\n",
       " 'ProcedureStepDescription': 'TA_VB17_FATAG1',\n",
       " 'SoftwareVersions': 'syngo_MR_B17',\n",
       " 'MRAcquisitionType': '2D',\n",
       " 'SeriesDescription': 'fieldmap56_DeltaTE1p02ms',\n",
       " 'ProtocolName': 'fieldmap56_DeltaTE1p02ms',\n",
       " 'ScanningSequence': 'GR',\n",
       " 'SequenceVariant': 'SP',\n",
       " 'SequenceName': '_fm2d2r',\n",
       " 'ImageType': ['ORIGINAL', 'PRIMARY', 'P', 'ND'],\n",
       " 'SeriesNumber': 6,\n",
       " 'AcquisitionTime': '08:58:10.132500',\n",
       " 'AcquisitionNumber': 1,\n",
       " 'SliceThickness': 3.2,\n",
       " 'SpacingBetweenSlices': 3.2,\n",
       " 'SAR': 0.0520705,\n",
       " 'EchoNumber': 2,\n",
       " 'EchoTime': 0.00702,\n",
       " 'RepetitionTime': 1.5,\n",
       " 'FlipAngle': 72,\n",
       " 'PartialFourier': 1,\n",
       " 'BaseResolution': 120,\n",
       " 'ShimSetting': [136, 312, 891, 657, -65, -296, 70, -44],\n",
       " 'TxRefAmp': 222.227,\n",
       " 'PhaseResolution': 1,\n",
       " 'ReceiveCoilName': '32Ch_Head_7T',\n",
       " 'PulseSequenceDetails': '%SiemensSeq%_gre_field_mapping',\n",
       " 'PercentPhaseFOV': 100,\n",
       " 'PhaseEncodingSteps': 120,\n",
       " 'AcquisitionMatrixPE': 120,\n",
       " 'ReconMatrixPE': 120,\n",
       " 'PixelBandwidth': 260,\n",
       " 'DwellTime': 1.6e-05,\n",
       " 'PhaseEncodingDirection': 'j-',\n",
       " 'ImageOrientationPatientDICOM': [0.999173,\n",
       "  -0.0383709,\n",
       "  0.0134587,\n",
       "  0.040655,\n",
       "  0.949164,\n",
       "  -0.312146],\n",
       " 'InPlanePhaseEncodingDirectionDICOM': 'COL',\n",
       " 'ConversionSoftware': 'dcm2niix',\n",
       " 'ConversionSoftwareVersion': 'v1.0.20180918  GCC5.4.0',\n",
       " 'EchoTime1': 0.006,\n",
       " 'EchoTime2': 0.00702,\n",
       " 'IntendedFor': ['ses-me/func/sub-01_ses-me_task-stop_run-1_echo-1_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-1_echo-2_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-1_echo-3_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-2_echo-1_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-2_echo-2_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-2_echo-3_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-3_echo-1_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-3_echo-2_bold.nii',\n",
       "  'ses-me/func/sub-01_ses-me_task-stop_run-3_echo-3_bold.nii']}"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "with open('./data/raw/bids/sub-01/ses-me/fmap/sub-01_ses-me_phasediff.json', 'r') as f:\n",
    "    d = json.load(f)\n",
    "d"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "bids_root = './data/raw/bids'\n",
    "dataset_descr = {'Name': 'IMCN Stop Task fMRI protocol comparison',\n",
    "                  'BIDSVersion': \"1.51.0.0-rc1\",\n",
    "                  'Authors': ['Steven Miletic',\n",
    "                              'Pierre-Louis Bazin',\n",
    "                              'Nikolaus Weiskopf',\n",
    "                              'Wietske van der Zwaag',\n",
    "                              'Birte U. Forstmann',\n",
    "                              'Robert Trampel'],\n",
    "                  'HowToAckowledge': 'Please cite the corresponding paper.'}\n",
    "import json\n",
    "with open(os.path.join(bids_root, 'dataset_description.json'), 'w') as f:\n",
    "    json.dump(dataset_descr, f)"
   ]
  }
 ],
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