Table 1

Participant inclusion and exclusion criteria for study

Inclusion	Exclusion
Outpatients 18–70 years of age (inclusive) at time of screening Meet DSM-V criteria for SUD at time of baseline visit. Criteria determined by the Structured Clinical Interview for DSM-V (SCID-5) which is a structured clinical interview used to confirm SUD diagnosis Veterans will not be excluded for comorbid substance use (ie, additional substance use beyond alcohol, cocaine or opiates), but data will be collected on use patterns so that these behaviours may be balanced across conditions and/or controlled for statistically Abstinent from alcohol for at least 3 days prior to baseline sTMS procedures; abstinent from benzodiazepines if meeting criteria for benzodiazepine use disorder Be on a stable psychotropic medication regimen for at least 6 weeks prior to baseline, or no psychotropic medication at all (for at least 6 weeks prior to baseline), and be willing to maintain the current regimen and dosing for the duration of the study (unless medically necessary to make changes) If there is a psychotropic medication change during the 6 weeks of sTMS treatment, the participants will notify the study team. If of childbearing potential, agree to use an acceptable method of birth control for the duration of the study treatment period Be willing and able to comply with all study-related procedures and visits Be capable of independently reading and understanding patient information materials and giving written informed consent Currently assigned a VA mental health treatment coordinator and willing to remain in care throughout the study Be willing to provide two verifiable emergency contacts	Any history of TBI with a severity greater than mild This will be defined by meeting any of the following criteria: (a) history of losing consciousness due to head injury for greater than 10 min; (b) history of losing consciousness due to a head injury with documented evidence of brain injury (including brain atrophy); (c) history of three or more concussions within the span of 1 year. Current (or past if appropriate) significant neurological disorder, or lifetime history of (a) seizure disorder, (b) primary or secondary CNS tumours, (c) stroke or (d) cerebral aneurysm Implanted devices activated or controlled by physiological signals, such as cardiac pacemakers, implanted medication pumps and intracardiac lines Participants must also not have an implanted device (deep brain stimulation) or metal in the following areas: brain, cervical spinal cord or upper thoracic spinal cord. Have metal objects lodged in their body, such as shrapnel, bullets or bullet fragments, or magnetically activated dental implants Significant alcohol withdrawal symptoms at baseline >1 month of abstinence from alcohol prior to baseline Are pregnant or lactating, or planning to become pregnant within 3 months after baseline Legally mandated substance abuse treatment Inability to obtain EEG of sufficient quality and duration that can be processed for use to calibrate the study device Unstable medical illness, or, in the opinion of the investigator, significant absence of appropriate medical care Current Axis 1 primary psychotic disorder, or bipolar I disorder Have active suicidal intent or plan, or in the investigative team’s opinion, is likely to attempt suicide within the next 6 months. Criteria determined by the SCID-5, which asks specifically about suicidal ideation (both passive and active), suicide plans and previous suicide attempts. Demonstrate the presence of any other condition or circumstance that, in the opinion of the investigative team, has the potential to prevent study completion and/or to have a confounding effect on outcome assessments

Inclusion

Exclusion

Outpatients 18–70 years of age (inclusive) at time of screening
Meet DSM-V criteria for SUD at time of baseline visit. Criteria determined by the Structured Clinical Interview for DSM-V (SCID-5) which is a structured clinical interview used to confirm SUD diagnosis
Veterans will not be excluded for comorbid substance use (ie, additional substance use beyond alcohol, cocaine or opiates), but data will be collected on use patterns so that these behaviours may be balanced across conditions and/or controlled for statistically
Abstinent from alcohol for at least 3 days prior to baseline sTMS procedures; abstinent from benzodiazepines if meeting criteria for benzodiazepine use disorder
Be on a stable psychotropic medication regimen for at least 6 weeks prior to baseline, or no psychotropic medication at all (for at least 6 weeks prior to baseline), and be willing to maintain the current regimen and dosing for the duration of the study (unless medically necessary to make changes) If there is a psychotropic medication change during the 6 weeks of sTMS treatment, the participants will notify the study team.
If of childbearing potential, agree to use an acceptable method of birth control for the duration of the study treatment period
Be willing and able to comply with all study-related procedures and visits
Be capable of independently reading and understanding patient information materials and giving written informed consent
Currently assigned a VA mental health treatment coordinator and willing to remain in care throughout the study
Be willing to provide two verifiable emergency contacts

Any history of TBI with a severity greater than mild This will be defined by meeting any of the following criteria: (a) history of losing consciousness due to head injury for greater than 10 min; (b) history of losing consciousness due to a head injury with documented evidence of brain injury (including brain atrophy); (c) history of three or more concussions within the span of 1 year.
Current (or past if appropriate) significant neurological disorder, or lifetime history of (a) seizure disorder, (b) primary or secondary CNS tumours, (c) stroke or (d) cerebral aneurysm
Implanted devices activated or controlled by physiological signals, such as cardiac pacemakers, implanted medication pumps and intracardiac lines Participants must also not have an implanted device (deep brain stimulation) or metal in the following areas: brain, cervical spinal cord or upper thoracic spinal cord.
Have metal objects lodged in their body, such as shrapnel, bullets or bullet fragments, or magnetically activated dental implants
Significant alcohol withdrawal symptoms at baseline
>1 month of abstinence from alcohol prior to baseline
Are pregnant or lactating, or planning to become pregnant within 3 months after baseline
Legally mandated substance abuse treatment
Inability to obtain EEG of sufficient quality and duration that can be processed for use to calibrate the study device
Unstable medical illness, or, in the opinion of the investigator, significant absence of appropriate medical care
Current Axis 1 primary psychotic disorder, or bipolar I disorder
Have active suicidal intent or plan, or in the investigative team’s opinion, is likely to attempt suicide within the next 6 months. Criteria determined by the SCID-5, which asks specifically about suicidal ideation (both passive and active), suicide plans and previous suicide attempts.
Demonstrate the presence of any other condition or circumstance that, in the opinion of the investigative team, has the potential to prevent study completion and/or to have a confounding effect on outcome assessments

CNS, central nervous system; DSM-V, Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition; EEG, electroencephalography; sTMS, synchronised transcranial magnetic stimulation; SUD, substance use disorder; TBI, traumatic brain injury; VA, Veterans Affairs.