BRIGhTMIND Trial Processing Pipeline

Table of Contents

• Prerequisities
• Script Usage
• Landmark Definition
• Background Threshold Definition
• Register Participant and Target in StimGuide™

Prerequisities

The BRIGhTMIND Trial Processing Pipeline has the following software requirements:

1. A 64-bit Linux Operating System

2. BRC Pipeline. During the trial, version 1.2.6 was used and therefore is the version that should be used to replicate results.

   • The BRC Pipeline has also its own software requirements.

3. MATLAB R2017b or later.

4. Python version 2.7 (the scripts should in principle also work with modern versions of Python (e.g. Python 3.x), but this has not been tested).

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Script Usage

Before running this script, the structural and resting-state fMRI datasets of the subject to process must be run through the BRC Pipeline's structural BRC_structural_pipeline/struc_preproc.sh and functional BRC_functional_pipeline/fMRI_preproc.sh procedures, respectively (in that order).

The following calls to BRC Pipeline were used in the BRIGhTMIND study:

• Structural pipeline (replace italicised parameters with actual values according to your data)

struc_preproc.sh --input <path_to_T1w_nifti> \
		 --path <brc_output_path> \
		 --subject <subject id> \
		 --strongbias \
		 --nodefacing

• Functional pipeline (replace italicised parameters with actual values according to your data)

fMRI_preproc.sh --fmripath <path_to_rsfMRI_nifti> \
		--path <brc_output_path> \
		--subject <subject id> \
		--mctype MCFLIRT6 \
		--dcmethod TOPUP \
		--slice2vol \
		--slspec <dcm2niix_json_file_for_rsfMRI> \
		--fwhm 5 \
		--echospacing <effective_echo_spacing_of_acquisition> \
		--stcmethod 1 \
		--SEPhasePos <path_to_rsfMRI_anterior_to_posterior_blip_nifti> \
		--SEPhaseNeg <path_to_rsfMRI_posterior_to_anterior_blip_nifti> \
		--unwarpdir y- \
		--biascorrection SEBASED \
		--echodiff NONE \
		--fmapmag NONE \
		--tempfilter 100

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The usage of run_brightmind_pipeline.sh is as follows:

     run_brightmind_pipeline.sh <arguments>

• Compulsory arguments (You MUST set all of):

    --path <brc_output_path>           BRC Pipeline output path
    --subject <subject id>             Subject ID as set in BRC Pipeline
    --landmarks-file <file path>       Text file containing the coordinates in mm of the nasion and preauricular points
    --background-thresh <value>        Integer specifying the intensity threshold between head and background on subject T1w image
  

• Optional arguments (You may optionally specify one or more of):

    --output-path <path>               Path of the folder where the compressed directories with StimGuide files are written (Default: 'StimGuide' folder inside subject directory)
    --fmri-folder-name <folder name>   Name of the fMRI folder from the BRC functional analysis pipeline. Default: 'rfMRI'"
    -h | --help                        help
  

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Landmark Definition

The BRIGhTMIND processing pipeline requires as input a text file with the location in mm of the nasion, left preauricular point and right preauricular point. In order to create this file, open the file <brc_output_path>/<subject id>/analysis/anatMRI/T1/processed/data/T1.nii.gz in your favourite NIFTI image viewer.

Location of the nasion

Locate the nasion as shown in the image below and take note of the X, Y and Z coordinates in mm

Location of the left/right preauricular points

Locate the left/right preauricular points as shown in the image below and take note of the X, Y and Z coordinates in mm

Landmark File

The final landmark file should look like the image below. The first line corresponds to the nasion coordinates, the second line to the left preauricular point coordinates and the third line to the right preauricular point coordinates.

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Background Threshold Definition

Another mandatory input to the BRIGhTMIND pipeline is an integer number defining the threshold between background and foreground in the T1-weighted structural image. In general terms, the procedure to determine this number is as follows:

1. Open the file <brc_output_path>/<subject id>/analysis/anatMRI/T1/processed/data/T1.nii.gz in your favourite NIFTI image viewer.

2. Window the image by lowering the maximum intensity, such that the skull/scalp has a clear boundary with the background, but at the same time there is not too much noise near the skull/scalp like in the example below:

   

3. The maximum intensity selected is the number to input into the script.

After the pipeline is run, the resulting GIFTI mesh <brc_output_path>/<subject id>/surf/lh.seghead.surf.gii should look smooth and complete like in the example below:

If the threshold number is set too low, the resulting scalp mesh may become too noisy like in this example:

If the threshold number is set too high, the resulting scalp mesh may be not complete and have holes in it.

Register Participant and Target in StimGuide™

1. Open StimGuide™
2. Register a new patient by clicking on "Register New Patient" and typing the same Subject ID used for the pipeline as Patient Identifier
3. Close StimGuide™
4. Create a "Targets" folder inside Documents\EzGuide\Studies\<subject id>\, where the "Documents" folder corresponds to the Microsoft Windows "Documents" folder of the user installed on the StimGuide™ computer.
5. Find the pipeline output folder (by default <brc_output_path>/<subject id>/StimGuide) and copy the ZIP file corresponding to the treatment arm you would like to use (rTMS or cgiTBS) to a USB stick or similar.
6. Plug the USB stick on the StimGuide™ computer and unzip the contents of the ZIP file (one .asc and one .xml file) into Documents\EzGuide\Studies\<subject id>\Targets.