fMRIPrep.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<p style='text-align:center'>\n",
    "PSY 394U <b>Methods for fMRI</b>, Fall 2019\n",
    "\n",
    "\n",
    "<img style='width: 300px; padding: 0px;' src='https://github.com/sathayas/JupyterfMRIFall2019/blob/master/Images/Placebo_Left.png?raw=true' alt='brain blobs'/>\n",
    "\n",
    "</p>\n",
    "\n",
    "<p style='text-align:center; font-size:40px; margin-bottom: 30px;'><b> fMRIPrep </b></p>\n",
    "\n",
    "<p style='text-align:center; font-size:18px; margin-bottom: 32px;'><b> October 7, 2019 </b></p>\n",
    "\n",
    "<hr style='height:5px;border:none' />"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# What is fMRIPrep?\n",
    "<hr style=\"height:1px;border:none\" />\n",
    "\n",
    "As you saw in the previous class, writing your own script for fMRI data pre-processing is a laborious work. Fortunately, there are a number of pre-processing tools written by others. If you choose to use such a tool, then you just run the tool and your data is pre-processed, ready to be analyzed. \n",
    "\n",
    "Your lab may have an fMRI pre-processing script handed down through generations of previous graduate students and post-docs. (I may be wrong, but) Such scripts are often based on a single software tool (probably either SPM or FSL). However, in recent years, it is becoming more common to mix and match different pre-processing steps from multiple software tools. fMRIPrep is a great example of that. \n",
    "\n",
    "**fMRIPrep** is a popular tool for fMRI data pre-processing. It combines multiple brain image processing tools to normalize T1-weighted images and fMRI data into the MNI template space. The default pipeline in fMRIPrep consists of FreeSurfer (surface extraction), ANTS (warping), FSL (segmentation), AFNI (physiological noise correction), and a number of other tools. You can pre-process your fMRI data (along with the accompanying T1 images) as long as your data set is organized in the BIDS structure. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Setting up fMRIPrep\n",
    "<hr style=\"height:1px;border:none\" />\n",
    "\n",
    "If you choose to run fMRIPrep on your computer, you need to set up fMRIPrep on your computer first. *As I mentioned in the syllabus, fMRIPrep is **optional** in this course.*\n",
    "\n",
    "## fMRIPrep Docker image\n",
    "To run fMRIPrep Docker image, you have to *pull* the docker image from the Docker Hub with the command:\n",
    "```\n",
    "docker pull poldracklab/fmriprep\n",
    "```\n",
    "This Docker image is rather large (~6GB).\n",
    "\n",
    "\n",
    "## FreeSurfer license\n",
    "\n",
    "Some of the default processing steps on fMRIPrep uses FreeSurfer. FreeSurfer is freely available, but you need a license file to run it. To get a license file, you have to register at https://surfer.nmr.mgh.harvard.edu/registration.html . A license file will be sent to you by email. ***You do not have to install FreeSurfer on your computer!*** FreeSurfer is included as part of the fMRIPrep Docker image. You just need the license file to run it."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Running fMRIPrep\n",
    "<hr style=\"height:1px;border:none\" />\n",
    "\n",
    "If you have followed the steps described in the previous section, you are ready to run fMRIPrep!\n",
    "\n",
    "## Docker command\n",
    "The fMRIPrep documentation suggests that you install a Python wrapper on your computer to run fMRIPrep. But that means installing Python on your computer. Alternatively, you can run the fMRIPrep Docker image directly the following command:\n",
    "```\n",
    "docker run --rm -it  --privileged -e DOCKER_VERSION_8395080871=1.13.1 \\\n",
    "-v [Path to FreeSurfer licence file]:/opt/freesurfer/license.txt:ro \\\n",
    "-v [Path to the data folder]:/data:ro \\\n",
    "-v [Path to the output folder]:/out \\\n",
    "poldracklab/fmriprep /data /out participant --participant-label 09\n",
    "```\n",
    "\n",
    "Here, `[Path to FreeSurfer licence file]` refers to the location of the aforementioned FreeSurfer license file on your local computer. `[Path to the data folder]` refers to where you store your data on your local computer. ***The data set has to follow the BIDS structure***. And `[Path to the output folder]` refers to the location where you want the output files / directories to be. The parameter **`--participant-label`** is necessary only when you want to run a single subject (as opposed to the entire data set). In this particular example, we analyze the data from subject **`09`**.\n",
    "\n",
    "The preprocessing steps involved in fMRIPrep are rather computationally intensive. So I will not run it right now, but will go over the results that I have previously run. For the sake of demonstration, I have run the `ds114` (test-retest) data set, subject 09. Just FYI, running this subject took about 5.5 hours on my Linux server (Centos 7, Intel Xeon 3.0GHz with 10 cores and 64GB of RAM). "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Output from fMRIPrep\n",
    "<hr style=\"height:1px;border:none\" />\n",
    "\n",
    "## Going over the summary\n",
    "So, assume we have been able to run this subject's preprocessing with fMRIPrep. We can examine the output from the preprocessing via the summary generated by fMRIPrep. It's in the form of an HTML file, so you can examine it on your web browser.\n",
    "\n",
    "[Summary generated by fMRIPrep](sub-09.html)\n",
    "\n",
    "\n",
    "## Resulting files\n",
    "fMRIPrep produces a large number of files. Here is a list of files and directories generated by fMRIPrep:\n",
    "```\n",
    "fmriprep/sub-09\n",
    "├── anat\n",
    "│   ├── sub-09_desc-aparcaseg_dseg.nii.gz\n",
    "│   ├── sub-09_desc-aseg_dseg.nii.gz\n",
    "│   ├── sub-09_desc-brain_mask.json\n",
    "│   ├── sub-09_desc-brain_mask.nii.gz\n",
    "│   ├── sub-09_desc-preproc_T1w.json\n",
    "│   ├── sub-09_desc-preproc_T1w.nii.gz\n",
    "│   ├── sub-09_dseg.nii.gz\n",
    "│   ├── sub-09_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5\n",
    "│   ├── sub-09_from-T1w_to-fsnative_mode-image_xfm.txt\n",
    "│   ├── sub-09_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5\n",
    "│   ├── sub-09_hemi-L_inflated.surf.gii\n",
    "│   ├── sub-09_hemi-L_midthickness.surf.gii\n",
    "│   ├── sub-09_hemi-L_pial.surf.gii\n",
    "│   ├── sub-09_hemi-L_smoothwm.surf.gii\n",
    "│   ├── sub-09_hemi-R_inflated.surf.gii\n",
    "│   ├── sub-09_hemi-R_midthickness.surf.gii\n",
    "│   ├── sub-09_hemi-R_pial.surf.gii\n",
    "│   ├── sub-09_hemi-R_smoothwm.surf.gii\n",
    "│   ├── sub-09_label-CSF_probseg.nii.gz\n",
    "│   ├── sub-09_label-GM_probseg.nii.gz\n",
    "│   ├── sub-09_label-WM_probseg.nii.gz\n",
    "│   ├── sub-09_space-MNI152NLin2009cAsym_desc-brain_mask.json\n",
    "│   ├── sub-09_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz\n",
    "│   ├── sub-09_space-MNI152NLin2009cAsym_desc-preproc_T1w.json\n",
    "│   ├── sub-09_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz\n",
    "│   ├── sub-09_space-MNI152NLin2009cAsym_dseg.nii.gz\n",
    "│   ├── sub-09_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz\n",
    "│   ├── sub-09_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz\n",
    "│   └── sub-09_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz\n",
    "├── figures\n",
    "│   ├── sub-09_desc-reconall_T1w.svg\n",
    "│   ├── sub-09_dseg.svg\n",
    "│   └── sub-09_space-MNI152NLin2009cAsym_T1w.svg\n",
    "├── ses-retest\n",
    "│   ├── anat\n",
    "│   │   └── sub-09_ses-retest_from-orig_to-T1w_mode-image_xfm.txt\n",
    "│   ├── figures\n",
    "│   │   ├── sub-09_ses-retest_task-covertverbgeneration_desc-bbregister_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-covertverbgeneration_desc-carpetplot_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-covertverbgeneration_desc-compcorvar_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-covertverbgeneration_desc-confoundcorr_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-covertverbgeneration_desc-rois_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-fingerfootlips_desc-bbregister_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-fingerfootlips_desc-carpetplot_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-fingerfootlips_desc-compcorvar_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-fingerfootlips_desc-confoundcorr_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-fingerfootlips_desc-rois_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-linebisection_desc-bbregister_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-linebisection_desc-carpetplot_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-linebisection_desc-compcorvar_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-linebisection_desc-confoundcorr_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-linebisection_desc-rois_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-overtverbgeneration_desc-bbregister_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-overtverbgeneration_desc-carpetplot_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-overtverbgeneration_desc-compcorvar_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-overtverbgeneration_desc-confoundcorr_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-overtverbgeneration_desc-rois_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-overtwordrepetition_desc-bbregister_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-overtwordrepetition_desc-carpetplot_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-overtwordrepetition_desc-compcorvar_bold.svg\n",
    "│   │   ├── sub-09_ses-retest_task-overtwordrepetition_desc-confoundcorr_bold.svg\n",
    "│   │   └── sub-09_ses-retest_task-overtwordrepetition_desc-rois_bold.svg\n",
    "│   └── func\n",
    "│       ├── sub-09_ses-retest_task-covertverbgeneration_desc-confounds_regressors.json\n",
    "│       ├── sub-09_ses-retest_task-covertverbgeneration_desc-confounds_regressors.tsv\n",
    "│       ├── sub-09_ses-retest_task-covertverbgeneration_space-fsaverage5_hemi-L.func.gii\n",
    "│       ├── sub-09_ses-retest_task-covertverbgeneration_space-fsaverage5_hemi-R.func.gii\n",
    "│       ├── sub-09_ses-retest_task-covertverbgeneration_space-MNI152NLin2009cAsym_boldref.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-covertverbgeneration_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-covertverbgeneration_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-covertverbgeneration_space-MNI152NLin2009cAsym_desc-brain_mask.json\n",
    "│       ├── sub-09_ses-retest_task-covertverbgeneration_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-covertverbgeneration_space-MNI152NLin2009cAsym_desc-preproc_bold.json\n",
    "│       ├── sub-09_ses-retest_task-covertverbgeneration_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-fingerfootlips_desc-confounds_regressors.json\n",
    "│       ├── sub-09_ses-retest_task-fingerfootlips_desc-confounds_regressors.tsv\n",
    "│       ├── sub-09_ses-retest_task-fingerfootlips_space-fsaverage5_hemi-L.func.gii\n",
    "│       ├── sub-09_ses-retest_task-fingerfootlips_space-fsaverage5_hemi-R.func.gii\n",
    "│       ├── sub-09_ses-retest_task-fingerfootlips_space-MNI152NLin2009cAsym_boldref.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-fingerfootlips_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-fingerfootlips_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-fingerfootlips_space-MNI152NLin2009cAsym_desc-brain_mask.json\n",
    "│       ├── sub-09_ses-retest_task-fingerfootlips_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-fingerfootlips_space-MNI152NLin2009cAsym_desc-preproc_bold.json\n",
    "│       ├── sub-09_ses-retest_task-fingerfootlips_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-linebisection_desc-confounds_regressors.json\n",
    "│       ├── sub-09_ses-retest_task-linebisection_desc-confounds_regressors.tsv\n",
    "│       ├── sub-09_ses-retest_task-linebisection_space-fsaverage5_hemi-L.func.gii\n",
    "│       ├── sub-09_ses-retest_task-linebisection_space-fsaverage5_hemi-R.func.gii\n",
    "│       ├── sub-09_ses-retest_task-linebisection_space-MNI152NLin2009cAsym_boldref.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-linebisection_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-linebisection_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-linebisection_space-MNI152NLin2009cAsym_desc-brain_mask.json\n",
    "│       ├── sub-09_ses-retest_task-linebisection_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-linebisection_space-MNI152NLin2009cAsym_desc-preproc_bold.json\n",
    "│       ├── sub-09_ses-retest_task-linebisection_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-overtverbgeneration_desc-confounds_regressors.json\n",
    "│       ├── sub-09_ses-retest_task-overtverbgeneration_desc-confounds_regressors.tsv\n",
    "│       ├── sub-09_ses-retest_task-overtverbgeneration_space-fsaverage5_hemi-L.func.gii\n",
    "│       ├── sub-09_ses-retest_task-overtverbgeneration_space-fsaverage5_hemi-R.func.gii\n",
    "│       ├── sub-09_ses-retest_task-overtverbgeneration_space-MNI152NLin2009cAsym_boldref.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-overtverbgeneration_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-overtverbgeneration_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-overtverbgeneration_space-MNI152NLin2009cAsym_desc-brain_mask.json\n",
    "│       ├── sub-09_ses-retest_task-overtverbgeneration_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-overtverbgeneration_space-MNI152NLin2009cAsym_desc-preproc_bold.json\n",
    "│       ├── sub-09_ses-retest_task-overtverbgeneration_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-overtwordrepetition_desc-confounds_regressors.json\n",
    "│       ├── sub-09_ses-retest_task-overtwordrepetition_desc-confounds_regressors.tsv\n",
    "│       ├── sub-09_ses-retest_task-overtwordrepetition_space-fsaverage5_hemi-L.func.gii\n",
    "│       ├── sub-09_ses-retest_task-overtwordrepetition_space-fsaverage5_hemi-R.func.gii\n",
    "│       ├── sub-09_ses-retest_task-overtwordrepetition_space-MNI152NLin2009cAsym_boldref.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-overtwordrepetition_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-overtwordrepetition_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-overtwordrepetition_space-MNI152NLin2009cAsym_desc-brain_mask.json\n",
    "│       ├── sub-09_ses-retest_task-overtwordrepetition_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz\n",
    "│       ├── sub-09_ses-retest_task-overtwordrepetition_space-MNI152NLin2009cAsym_desc-preproc_bold.json\n",
    "│       └── sub-09_ses-retest_task-overtwordrepetition_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz\n",
    "└── ses-test\n",
    "    ├── anat\n",
    "    │   └── sub-09_ses-test_from-orig_to-T1w_mode-image_xfm.txt\n",
    "    ├── figures\n",
    "    │   ├── sub-09_ses-test_task-covertverbgeneration_desc-bbregister_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-covertverbgeneration_desc-carpetplot_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-covertverbgeneration_desc-compcorvar_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-covertverbgeneration_desc-confoundcorr_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-covertverbgeneration_desc-rois_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-fingerfootlips_desc-bbregister_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-fingerfootlips_desc-carpetplot_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-fingerfootlips_desc-compcorvar_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-fingerfootlips_desc-confoundcorr_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-fingerfootlips_desc-rois_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-linebisection_desc-bbregister_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-linebisection_desc-carpetplot_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-linebisection_desc-compcorvar_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-linebisection_desc-confoundcorr_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-linebisection_desc-rois_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-overtverbgeneration_desc-bbregister_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-overtverbgeneration_desc-carpetplot_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-overtverbgeneration_desc-compcorvar_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-overtverbgeneration_desc-confoundcorr_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-overtverbgeneration_desc-rois_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-overtwordrepetition_desc-bbregister_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-overtwordrepetition_desc-carpetplot_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-overtwordrepetition_desc-compcorvar_bold.svg\n",
    "    │   ├── sub-09_ses-test_task-overtwordrepetition_desc-confoundcorr_bold.svg\n",
    "    │   └── sub-09_ses-test_task-overtwordrepetition_desc-rois_bold.svg\n",
    "    └── func\n",
    "        ├── sub-09_ses-test_task-covertverbgeneration_desc-confounds_regressors.json\n",
    "        ├── sub-09_ses-test_task-covertverbgeneration_desc-confounds_regressors.tsv\n",
    "        ├── sub-09_ses-test_task-covertverbgeneration_space-fsaverage5_hemi-L.func.gii\n",
    "        ├── sub-09_ses-test_task-covertverbgeneration_space-fsaverage5_hemi-R.func.gii\n",
    "        ├── sub-09_ses-test_task-covertverbgeneration_space-MNI152NLin2009cAsym_boldref.nii.gz\n",
    "        ├── sub-09_ses-test_task-covertverbgeneration_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz\n",
    "        ├── sub-09_ses-test_task-covertverbgeneration_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz\n",
    "        ├── sub-09_ses-test_task-covertverbgeneration_space-MNI152NLin2009cAsym_desc-brain_mask.json\n",
    "        ├── sub-09_ses-test_task-covertverbgeneration_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz\n",
    "        ├── sub-09_ses-test_task-covertverbgeneration_space-MNI152NLin2009cAsym_desc-preproc_bold.json\n",
    "        ├── sub-09_ses-test_task-covertverbgeneration_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz\n",
    "        ├── sub-09_ses-test_task-fingerfootlips_desc-confounds_regressors.json\n",
    "        ├── sub-09_ses-test_task-fingerfootlips_desc-confounds_regressors.tsv\n",
    "        ├── sub-09_ses-test_task-fingerfootlips_space-fsaverage5_hemi-L.func.gii\n",
    "        ├── sub-09_ses-test_task-fingerfootlips_space-fsaverage5_hemi-R.func.gii\n",
    "        ├── sub-09_ses-test_task-fingerfootlips_space-MNI152NLin2009cAsym_boldref.nii.gz\n",
    "        ├── sub-09_ses-test_task-fingerfootlips_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz\n",
    "        ├── sub-09_ses-test_task-fingerfootlips_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz\n",
    "        ├── sub-09_ses-test_task-fingerfootlips_space-MNI152NLin2009cAsym_desc-brain_mask.json\n",
    "        ├── sub-09_ses-test_task-fingerfootlips_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz\n",
    "        ├── sub-09_ses-test_task-fingerfootlips_space-MNI152NLin2009cAsym_desc-preproc_bold.json\n",
    "        ├── sub-09_ses-test_task-fingerfootlips_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz\n",
    "        ├── sub-09_ses-test_task-linebisection_desc-confounds_regressors.json\n",
    "        ├── sub-09_ses-test_task-linebisection_desc-confounds_regressors.tsv\n",
    "        ├── sub-09_ses-test_task-linebisection_space-fsaverage5_hemi-L.func.gii\n",
    "        ├── sub-09_ses-test_task-linebisection_space-fsaverage5_hemi-R.func.gii\n",
    "        ├── sub-09_ses-test_task-linebisection_space-MNI152NLin2009cAsym_boldref.nii.gz\n",
    "        ├── sub-09_ses-test_task-linebisection_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz\n",
    "        ├── sub-09_ses-test_task-linebisection_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz\n",
    "        ├── sub-09_ses-test_task-linebisection_space-MNI152NLin2009cAsym_desc-brain_mask.json\n",
    "        ├── sub-09_ses-test_task-linebisection_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz\n",
    "        ├── sub-09_ses-test_task-linebisection_space-MNI152NLin2009cAsym_desc-preproc_bold.json\n",
    "        ├── sub-09_ses-test_task-linebisection_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz\n",
    "        ├── sub-09_ses-test_task-overtverbgeneration_desc-confounds_regressors.json\n",
    "        ├── sub-09_ses-test_task-overtverbgeneration_desc-confounds_regressors.tsv\n",
    "        ├── sub-09_ses-test_task-overtverbgeneration_space-fsaverage5_hemi-L.func.gii\n",
    "        ├── sub-09_ses-test_task-overtverbgeneration_space-fsaverage5_hemi-R.func.gii\n",
    "        ├── sub-09_ses-test_task-overtverbgeneration_space-MNI152NLin2009cAsym_boldref.nii.gz\n",
    "        ├── sub-09_ses-test_task-overtverbgeneration_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz\n",
    "        ├── sub-09_ses-test_task-overtverbgeneration_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz\n",
    "        ├── sub-09_ses-test_task-overtverbgeneration_space-MNI152NLin2009cAsym_desc-brain_mask.json\n",
    "        ├── sub-09_ses-test_task-overtverbgeneration_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz\n",
    "        ├── sub-09_ses-test_task-overtverbgeneration_space-MNI152NLin2009cAsym_desc-preproc_bold.json\n",
    "        ├── sub-09_ses-test_task-overtverbgeneration_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz\n",
    "        ├── sub-09_ses-test_task-overtwordrepetition_desc-confounds_regressors.json\n",
    "        ├── sub-09_ses-test_task-overtwordrepetition_desc-confounds_regressors.tsv\n",
    "        ├── sub-09_ses-test_task-overtwordrepetition_space-fsaverage5_hemi-L.func.gii\n",
    "        ├── sub-09_ses-test_task-overtwordrepetition_space-fsaverage5_hemi-R.func.gii\n",
    "        ├── sub-09_ses-test_task-overtwordrepetition_space-MNI152NLin2009cAsym_boldref.nii.gz\n",
    "        ├── sub-09_ses-test_task-overtwordrepetition_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz\n",
    "        ├── sub-09_ses-test_task-overtwordrepetition_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz\n",
    "        ├── sub-09_ses-test_task-overtwordrepetition_space-MNI152NLin2009cAsym_desc-brain_mask.json\n",
    "        ├── sub-09_ses-test_task-overtwordrepetition_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz\n",
    "        ├── sub-09_ses-test_task-overtwordrepetition_space-MNI152NLin2009cAsym_desc-preproc_bold.json\n",
    "        └── sub-09_ses-test_task-overtwordrepetition_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz\n",
    "\n",
    "10 directories, 194 files\n",
    "```\n",
    "\n",
    "Many many files! But here are some key things to remember:\n",
    "\n",
    "1. The overall organization is still similar to the original BIDS data directory. In other words, the parent directory is the study directory, then individual subject directories, then session directories.\n",
    "2. Under the session directories, you will find the **`func`** directory with pre-processed fMRI data for all runs and tasks.\n",
    "3. There is **`anat`** directory under each subject, containing all pre-processed T1-weighted images.\n",
    "\n",
    "For the analysis of the pre-processed fMRI data, you will only need a small number of files:\n",
    "\n",
    "* **fMRI**: The file with the suffix **`_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz`**.\n",
    "* **fMRI mask image**: The file with the suffix **`_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz`**\n",
    "* **T1w**: The file with the suffix **`_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz`**\n",
    "* **T1w mask image**: The file with the suffix **`_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz`**\n"
   ]
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