Single Subject Analysis: Visual/Motor Activation

Preprocessing a single subject/session and applying a general linear model using AFNI

Step 1: Download data from XNAT and automatically convert to BIDS format with xnat-tools

In this example, we will use the data from demodat2 participant 101, session 1. Running the following series of commands on the command line in Oscar will download the data we need, convert it to BIDS format, and run the BIDS validator to check for any issues. We will be using the xnat-tools Oscar utility script explained here.

First, we need to create a configuration .toml file that contains some information xnat-tools needs to download the correct data and put it where we want. Let's call this file x2b_demodat2_config.toml and place wherever you'd like (simplest would be your home directory). Paste the following into your .toml file, and change mail-user to your email address. The script will default to placing the downloaded and BIDS-converted data in a folder called "bids-export" in your home directory; if you'd like to change this location, add a new line at the bottom with your desired path, i.e.: bids_root="/oscar/home/<yourusername>/xnat-export". Make sure to save this .toml file when you are done editing.

# Configuring arguments here will override default parameters.
[slurm-args]
mail-user = "[email protected]"
mail-type = "ALL"

[xnat2bids-args]
sessions = [
    "XNAT_E01849"
    ]
# Skip scanner-derived multi-planar reconstructions & non-distortion-corrected images 
# These are used for MRS voxel placement on the scanner and will cause xnat2bids to fail. 
skipseq=["anat-t1w_acq-memprage_MPR_Cor","anat-t1w_acq-memprage_MPR_Tra","anat-t1w_acq-memprage_MPR_Tra_ND","anat-t1w_acq-memprage RMS_ND","anat-t1w_acq-memprage_MPR_Cor_ND"]
verbose=1

To run the xnat-tools export and BIDS conversion, change directory to /oscar/data/bnc/shared/scripts/. On the command line, type:

module load anaconda

python run_xnat2bids.py --config ~/x2b_demodat2_config.toml

If you named your .toml file differently or placed it somewhere other than your home directory, make sure to include the full path to your file and the correct filename. Enter your XNAT username and password when prompted.

You should receive output that looks like this:

Enter XNAT Username: example-username
Enter Password: 
DEBUG: {'message': 'Argument List', 'session': 'XNAT_E01849', 'slurm_param_list': ['--time 04:00:00', '--mem 16000', '--nodes 1', '--cpus-per-task 2', '--job-name xnat2bids', '--mail-user [email protected]', '--mail-type ALL', '--output /oscar/scratch/gleblan1/logs/%x-XNAT_E01849-%J.txt'], 'x2b_param_list': ['XNAT_E01849', '/oscar/home/gleblan1/data/Demodat2_documentation', '--user gleblan1', '--host "https://xnat.bnc.brown.edu"', '--skipseq 3 --skipseq 4 --skipseq 5 --skipseq 7 --skipseq 8 --skipseq 19 --skipseq 20 --skipseq 21', '--overwrite', '--verbose']}
DEBUG: {'message': 'Executing xnat2bids', 'session': 'XNAT_E01849', 'command': ['sbatch', '--time', '04:00:00', '--mem', '16000', '--nodes', '1', '--cpus-per-task', '2', '--job-name', 'xnat2bids', '--mail-user', '[email protected]', '--mail-type', 'ALL', '--output', '/oscar/scratch/gleblan1/logs/%x-XNAT_E01849-%J.txt', '--wrap', '""apptainer exec --no-home -B /oscar/home/gleblan1/data/Demodat2_documentation /oscar/data/bnc/simgs/brownbnc/xnat-tools-v1.7.2.sif xnat2bids XNAT_E01849 /oscar/home/gleblan1/data/Demodat2_documentation --user gleblan1 --pass [REDACTED] --host "https://xnat.bnc.brown.edu" --skipseq 3 --skipseq 4 --skipseq 5 --skipseq 7 --skipseq 8 --skipseq 19 --skipseq 20 --skipseq 21 --overwrite --verbose""']}
sbatch: slurm_job_submit: No partition specified, moved to batch.
sbatch: slurm_job_submit: No partition specified, moved to batch.
INFO: Launched 1 xnat2bids job
INFO: Job ID: 11854472
INFO: Launched bids-validator to check BIDS compliance
INFO: Job ID: 11854473
INFO: Processed Scans Located At: /oscar/home/example-username/bids-export

If you entered your email address, you should receive an email when your xnat2bids job begins, and another when it finishes.

This will create a sourcedata folder for subject 101 within $bids_root/bnc/study-demodat/xnat-export and a BIDS-compatible data directory for subject 101 within $bids_root/bnc/study-demodat/bids/.

We will call this output BIDS-compatible folder (/oscar/home/<yourusername>/xnat-export/bnc/study-demodat/bids/ , unless you specified a different $bids_root location) $bidsdir for the remainder of the tutorial.

Step 2: Extract stimulus timing information from stimulus presentation output files.

To make our data BIDS compatible and facilitate future data sharing, we need to create events.tsv files that correspond to each of our functional runs and contain information about each stimulus event of interest (onset time, condition, etc.). First, download the participant's data files (in our case, created by PsychoPy) and place them in the sourcedata subfolder of your BIDS directory in a subfolder named 'beh'. So, for this participant and session, the full path should be: $bidsdir/sourcedata/sub-101/ses-01/beh.

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sub-101_ses-01_beh.zip

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Demodat subject 101 session 01 behavioral data.

Next, download our example python script make_events.py, and run it from the command line with python make_events_LRChx.py --bids_dir $bidsdir --subj sub-101 --sess ses-01. For this script to run, you'll need both numpy and pandas installed in your python environment (if you're doing this on Oscar and you run module load anaconda/latest, you should be all set). This script will create BIDS-formatted events.tsv files corresponding to each functional run in $bidsdir/sub-101/ses-01/func/.

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make_events_LRChx.py

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Example python script to read in csv files created by PsychoPy and create the events.tsv files corresponding to each fMRI run

If you are unable to run this script for any reason, you can download the events.tsv output files here, and manually place them in $bidsdir/sub-101/ses-01/func/ .

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sub-101_ses-01_eventsfiles.zip

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Step 3: Convert events.tsv files into AFNI stimulus timing files

We needed to make those events.tsv files for BIDS compatibility, but in order to run our statistical analysis in AFNI, we need to transform them into .1D text files required by AFNI for specifying stimulus timing information. Instead of one file per run, as we had with the events.tsv files, here we need one file per condition (e.g. left hemifield checks or right button presses). These files are formatted to have one line per run of the task, specifying all the onset times for that condition. Since we collected two runs of the functional tasks, there should be two lines in this file. We have created an example python script make_afni_stimtimes_LRChx.py, which you can run from the command line just as you did make_events.py: python make_afni_stimtimes_LRChx.py --bids_dir $bidsdir --subj sub-101 --sess ses-01 . This will create stimulus timing files in $bidsdir/derivatives/afni/sub-101/ses-01/stimtimes/ .

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make_afni_stimtimes_LRChx.py

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example python script to read in events.tsv files from each functional run and output the .1D stimulus timing files AFNI needs

If you are unable to run this script for any reason, you can download the .1D files here and manually place them in $bidsdir/derivatives/afni/sub-101/ses-01/stimtimes/.

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sub-101_ses-01_stimtimes.zip

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Step 4: Use afni_proc.py to create a simple preprocessing stream and run the general linear model for the checks task

To access AFNI on Oscar, type module load afni.

This basic example of a univariate analysis with AFNI is based on the example 6b for afni_proc.py. The -blocks flag lists the processing blocks that will be executed, in order:

1. tshift (slice time correction)

2. align (aligning the EPIs to the anatomical scan)

3. volreg (motion correction within each functional run)

4. blur (spatial smoothing with a 4mm FWHM smoothing kernel)

5. mask (create a "brain" mask from the functional data, restricted by the anatomy)

6. scale (scale each voxel to have a mean of 100 per run)

7. regress (build a general linear model and execute with 3dREMLfit)

For the visual hemifield localizer regression, we use:

-regress_stim_times to provide the stimulus timing files for this participant (sub-101_checks_left_stimtimes.1D and sub-101_checks_right_stimtimes.1D)

-regress_stim_labels to assign those conditions the labels of "leftchx" and "rightchx" respectively

-regress_basis to model each stimulus as a block lasting 12 seconds

-regress_opts_3dD to specify our contrasts. Here, we do a "left_vs_right_chx" contrast to find voxels whose activity is greater for the left hemifield stimulation than for the right.

For the motor task (keypress) regression, we use:

-regress_stim_times to provide the stimulus timing files for this participant (sub-101_keypress_left_stimtimes.1D and sub-101_keypress_right_stimtimes.1D)

-regress_stim_labels to assign those conditions the labels of "leftpress" and "rightpress" respectively

-regress_basis to model each stimulus as an instantaneous event (indicated by using AFNI's 'GAM' function)

-regress_opts_3dD to specify our contrasts. Here, we do a "left_vs_right_press" contrast to find voxels whose activity is greater for the left index finger motor activation than for the right.

Run the batch script

Copy the text in the box below into a file editor on Oscar. Change your email in the beginning section, and change the value of the bidsdir variable to your own location (path should end in /bids). Save this script as a file called demodat2_afniproc.sh, and then execute it on the command line with sbatch demodat2_afniproc.sh. It will launch as a batch script, similar to how xnat2bids is used. You will receive an email when the job has completed.

afniproc.py will create its output folders in the directory that it is run from. To ensure all outputs are organized in the appropriate BIDS derivatives folder, the batch script will navigate to the output directory before launching afniproc.py. Because of this, you can launch the batch script from any directory!

This demodat2_afniproc.sh script will create a much longer proc.sub-101_ses-01 tcsh script, which will be automatically executed because we included the -execute flag at the bottom of the script. Looking at the proc.sub-101_ses-01 script is the best way to gain a deeper understanding of each of AFNI's processing steps.

demodat2_afniproc.sh

#!/bin/bash
#SBATCH -N 1
#SBATCH -c 8
#SBATCH --mem=10G
#SBATCH --time 2:00:00
#SBATCH -J demodat2_afniproc_sub-101_ses-01
#SBATCH --output demodat2_afniproc_sub-101_ses-01-%J.txt
#SBATCH --mail-user [email protected]
#SBATCH --mail-type ALL

# This script runs GLM regressions for both the hemifield activation task (LRChx) and the motor task (key press). 

bidsdir='enter your $bidsdir path here'
subID='sub-101'
sess='ses-01'

#navigate to this subject/session's output directory
cd $bidsdir/derivatives/afni/$subID/$sess

module load afni

afni_proc.py                                                         \
    -subj_id                  ${subID}_${sess}                               \
    -out_dir                  $bidsdir/derivatives/afni/$subID/$sess/$subID.results  \
    -copy_anat                $bidsdir/$subID/$sess/anat/${subID}_${sess}_acq-memprageRMS_T1w.nii.gz        \
    -anat_has_skull           yes                                     \
    -dsets                    $bidsdir/$subID/$sess/func/*checks*nii*                 \
    -blocks                   tshift align volreg blur mask scale regress                          \
    -tcat_remove_first_trs    0                                      \
    -align_opts_aea           -cost lpc+ZZ                           \
                                -giant_move                            \
                                -check_flip                            \
    -volreg_align_to          MIN_OUTLIER                            \
    -volreg_align_e2a                                                \
    -mask_epi_anat            yes                                    \
    -blur_size                4.0                                    \
    -regress_stim_times       $bidsdir/derivatives/afni/$subID/$sess/stimtimes/${subID}_checks_left_stimtimes.1D $bidsdir/derivatives/afni/$subID/$sess/stimtimes/${subID}_checks_right_stimtimes.1D  \
                              $bidsdir/derivatives/afni/$subID/$sess/stimtimes/${subID}_keypress_left_stimtimes.1D $bidsdir/derivatives/afni/$subID/$sess/stimtimes/${subID}_keypress_right_stimtimes.1D   \
    -regress_stim_labels      leftchx rightchx leftpress rightpress                               \
    -regress_basis_multi      'BLOCK(12,1)' 'BLOCK(12,1)' 'GAM' 'GAM'                          \
    -regress_opts_3dD         -jobs 2                                \
                                -gltsym 'SYM: leftchx -rightchx'                \
                                -glt_label 1 left_vs_right_chx                       \
                                -gltsym 'SYM: leftpress -rightpress'     \
                                -glt_label 2 left_vs_right_press        \
    -regress_motion_per_run                                          \
    -regress_censor_motion    0.3                                    \
    -regress_censor_outliers  0.05                                   \
    -regress_reml_exec                                               \
    -regress_compute_fitts                                           \
    -regress_make_ideal_sum   sum_ideal.1D                           \
    -regress_est_blur_epits                                          \
    -regress_est_blur_errts                                          \
    -regress_run_clustsim     yes                                     \
    -html_review_style        pythonic                               \
    -execute

Step 5: Viewing the Output

Visual Hemifield Localizer Task

After the demodat2_afniproc.sh script executes successfully, a results directory will be created: $bidsdir/derivatives/afni/sub-101/ses-01/sub-101_results. Start AFNI from within this directory (just type afni on the command line), set the underlay to anat_final.sub-101_ses-01 and the overlay to stats.sub-101_ses-01_REML. In the Define Overlay menu, set the OLay to #13 left_vs_right_chx#0_Coef , the Thr to #13left_vs_right_chx#0_Tstat, and change the threshold to your desired alpha (here we've used p = 0.001). This left vs. right contrast shows regions of the brain that show a stronger BOLD response to left vs. right visual hemifield stimulation, so we can easily localize the right visual cortex and the right LGN, as expected.

Results of a general linear test contrasting left vs. right visual hemifield stimulation, in demodat subject 101 session 01

Motor Activation (Button Press) Task

To view the GLT results for left versus right button presses, change the overlay to #16left_vs_right_press#0_Coef and the Thr to #17left_vs_right_press#0_Tstat.