Cortical Functional Connectivity as an Early Biomarker of Recovery in Spinal Cord Injury (Study 239481)
Phase: NA
Conditions: Spinal Cord Injuries
Sponsor: Hugo W. Moser Research Institute at Kennedy Krieger, Inc.

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 1 of 17 
 
 
 
 
 
 
 
 
 
Title:   Cortical functional connectivity as an early biomarker of recovery in spinal 
cord injury 
  
Number:   IRB00182576 
 
Principal Investigator:   Ann Choe 
 
NCT Number: NCT03854214 
 
Approval Date: 11/29/2018 
 
Document Date: 4/14/2023 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 2 of 17 
 
 
JHM IRB - eForm A – Protocol 
 
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 When submitting JHM IRB eForm A (new or revised), enter the date submitted to the field at 
the top of JHM IRB eForm A. 
 
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1. 
Abstract 
a. Provide no more than a one page research abstract briefly stating the problem, the research 
hypothesis, and the importance of the research. 
 
Early detection of response to therapeutic intervention in patients with chronic spinal cord injury (SCI) is 
crucial, as it will enable early adjustment or termination of intervention in non-responding patients, 
minimizing undue stress and financial burden. The goal of this study is to establish resting state fMRI 
(rsfMRI) outcome measures as novel non-invasive imaging biomarkers for early prediction of neurological 
improvements in response to intervention.  
Cortical reorganization that occurs in SCI patients during therapeutic interventions underlies 
neurological and functional recovery. Thus, the ability to observe the degree of reorganization would allow 
investigation of therapeutically induced cortical changes in SCI patients that are predictive of recovery. 
Conventional fMRI allows observation of such changes using explicit tasks (task activated fMRI; tfMRI). 
However, SCI patients are often unable to complete the required tasks. tfMRI also has limited capacity to 
observe functional organization of the entire brain, making the method better suited to assess local regions. 
In contrast, rsfMRI doesn’t require explicit tasks. This has strong clinical appeal, as it allows the use of an 
identical protocol for all, regardless of the degree of physical limitations. Moreover, rsfMRI allows 
localization of functionally homogeneous regions (parcels) of the entire brain with a single image 
acquisition – providing the means to efficiently estimate cortical functional organization in a data-driven 
manner. Two popular categories of such parcellation approaches include Independent component analysis 
(ICA; a method that uses a blind source separation algorithm to identify intrinsic brain functional networks) 
and temporal clustering, such as spectral clustering analysis (SCA; a method that uses spectral clustering to 
identify spatially coherent brain parcels). To date, these parcellation approaches have not been used to 
investigate functional reorganization associated with post-SCI intervention. 
Functional electrical stimulation (FES) cycling is an intervention for SCI patients, in which patterned 
electrical pulses are delivered to lower extremity muscles to initiate cycling movement. Our group has 
shown that FES cycling, but not passive cycling (i.e., movement is driven only by the cycle’s motor, 
without electric stimulation), leads to improvements in sensorimotor function, as measured using the 
International Standard of Neurological Classification for Spinal Cord Injury (ISNCSCI) scoring system. 
Unfortunately, early detection of response to intervention using ISNCSCI alone is challenging, as 
observation of clinically significant improvement (increase in ISNCSCI scores) requires at least 4 weeks of 
intervention. In contrast, previous tfMRI studies have shown that cortical reorganization can be observed 
after as little as one week of intervention. We hypothesize that reorganization of the sensorimotor cortex 
underlies neurological and functional recovery during intervention, and that such cortical reorganization 
will occur prior to observation of clinical improvement. We therefore propose that rsfMRI outcome 
measures, such as between-network connectivity (BNC; calculated as the degree of temporal dependency 
between functional networks), can be used to detect early changes in brain functional networks that are 
predictive of recovery. 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 3 of 17 
 
If successful, these studies will: 1) provide a new and effective clinical tool to study plastic cortical 
changes that occur after SCI, 2) provide new imaging biomarkers that are predictive of progress towards 
recovery in response to therapy, and 3) extend our knowledge about the functional reorganization that takes 
place during and after therapeutic intervention. The developed methods may have broader applications in 
number of other diseases that affect motor functions, such as stroke and Parkinson’s disease. 
 
2. 
Objectives (include all primary and secondary objectives) 
 
Aim 1. Characterize the baseline time profile of the rsfMRI outcome measures in chronic SCI 
patients, acquired over 4 weeks of passive (sham) cycling. In order to quantitatively assess the sensitivity 
of rsfMRI outcome measures to early functional reorganization that occurs in response to FES cycling, 
baseline time profile of the outcome measures in the absence of the active stimulation must be established. 
Accordingly, patients will participate in a 4-week passive cycling program. At weeks 0, 2, and 4, sensory 
and motor network BNC (calculated using ICA- and SCA-derived brain parcels) and ISNCSCI scores will 
be measured. Hypothesis: we will observe stable baseline measures of sensory and motor cortex BNC and 
ISNCSCI scores of the patients during the 4-week passive cycling program, with minimal to no change in 
values. 
Aim 2. Characterize the time profile of the cortical reorganization in chronic SCI patients that 
occurs during a 4-week FES cycling program. Hypothesis: We will observe early sensorimotor cortex 
BNC changes after 2 weeks of FES cycling, that are predictive of changes in ISNCSCI scores at week 4. 
Specifically, we hypothesize that: a) Changes in sensory network BNC at week 2 will correlate with 
changes in sensory ISNCSCI scores at week 4; b) Changes in motor network BNC at week 2 will correlate 
with changes in motor ISNCSCI scores at week 4. To test these hypotheses, we will first measure the 
sensory and motor network BNC and ISNCSCI scores at weeks 0, 2, and 4, then correlate the changes in 
sensory and motor network BNC at week 2 with the changes in respective ISNCSCI scores at week 4. 
Finally, longitudinal (pre- and post- intervention) inter- and intra-subject reproducibility of the ICA- and 
SCA-derived parcels will be assessed. 
 
3. 
Background (briefly describe pre-clinical and clinical data, current experience with procedures, 
drug or device, and any other relevant information to justify the research) 
 
Spinal Cord Injury and Rehabilitation.  
There is a perception in the field that significant neurological recovery in chronic SCI patients is unlikely. 
Recent studies, however, suggest that continued rehabilitation may enable recovery of sensation, function, 
and mobility in chronic SCI patients, months and even years after injury; leading to increased interest in 
interventions for chronic patients. In particular, active rehabilitation therapy, which aims to induce 
neurological improvements through continued physical activity, is receiving renewed attention, as it can 
increase muscle mass and strength. Functional electrical stimulation (FES) cycling is a widely-adapted 
component of the active rehabilitation therapy. This approach uses small electrical pulses that are applied to 
lower extremity muscles to initiate cycling movement. Previous clinical and preclinical studies have shown 
that FES increases the degree of physical integrity and functional recovery in SCI. Also, in a recent 
retrospective cross-sectional clinical study, our group showed that FES cycling, but not passive cycling 
(i.e., movement is driven only by the cycle’s motor, without electric stimulation), leads to 80% composite 
motor-sensory score responder rate, higher quadriceps muscle mass (36%), higher muscle strength (35%), 
and higher quality of life and functional ability in SCI patients. As a widely-practiced component of the 
active rehabilitation therapy program with proven benefits for neurological recovery of chronic SCI 
patients, FES cycling is an excellent candidate for assessing the SCI patient response to an intervention 
program. 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 4 of 17 
 
The International Standard of Neurological Classification for Spinal Cord Injury (ISNCSCI) scoring 
system is the most widely used clinical classification system of SCI. However, monitoring of response to 
intervention using only ISNCSCI is challenging. While ISNCSCI is excellent in describing the neurological 
level of SCI, its ability to describe the degree of functional loss, and therefore the sensitivity to changes in 
function, is limited. This is a significant issue, as it prevents early detection of response to intervention. 
While alternative neurological assessment measures are available, unfortunately, acquisition of such 
measures is often time-consuming. Given these limitations of the currently available outcome measures for 
SCI interventions, there is a compelling clinical need for new biomarkers that are: 1) measurable in 
heterogeneous SCI patient cohorts, and 2) sensitive to early responses to SCI intervention programs. We 
hypothesize that resting state fMRI (rsfMRI) outcome measures will effectively fulfill these requirements. 
 
Resting State Functional MRI.  
In addition to the degree of structural integrity at the injury epicenter that directly contributes to the 
capacity for neurological recovery in SCI patients, changes in brain functional networks are also thought to 
affect functional and neurological recovery. For example, plastic changes of somatosensory representation 
within cortex have been extensively reported both in previous preclinical and clinical studies, which are 
thought to be caused by the increased utilization of spared parts of the body. Two task activated fMRI 
(tfMRI) studies by Jurkiewicz et al are particularly relevant, as they showed that SCI patients who 
experienced recovery demonstrated a progressive enlargement in the volume of movement-related primary 
motor cortex (M1) activation and decreased activation in associated cortical sensorimotor areas. In contrast, 
those who experienced persistent paralysis demonstrated activation in M1 that was significantly reduced 
and progressively decreased in associated cortical sensorimotor areas. Authors conclude that together, the 
results suggest an association between motor task-related fMRI activation and degree of motor function 
post-injury. However, whether and how the observed cortical changes contribute to recovery remains 
largely unexplored. Having the ability to observe the pattern and degree of cortical functional 
reorganization would enable us to study changes that may be predictive of progress towards recovery. 
In 1995, Biswal et al showed that blood oxygenation level dependent signals in functionally connected 
brain regions fluctuate in a highly correlated manner, even in the absence of explicit task performance 
(therefore the name “resting state” fMRI; rsfMRI). There are three major advantages of rsfMRI that are 
especially relevant to this project: 1) easy applicability to heterogeneous SCI cohorts: Unlike the 
conventional tfMRI, rsfMRI does not require explicit tasks. This allows the use of an identical protocol for 
patients in various stages of diseases and interventions, regardless of their degree of physical limitation. 2) 
capacity to observe functional organization within major brain networks within a clinically feasible 
timeframe: RsfMRI allows localization of functionally homogeneous regions (parcels) of the entire brain 
with a single image acquisition – providing the means to efficiently estimate cortical functional 
organization in a data-driven manner. Two popular categories of such parcellation approaches include 
Independent component analysis (ICA; a method that uses a blind source separation algorithm to identify 
intrinsic brain functional networks) and temporal clustering, such as spectral clustering analysis (SCA; a 
method that uses spectral clustering to identify spatially coherent brain parcels). To date, these parcellation 
approaches have not been used to investigate functional reorganization associated with post-SCI 
intervention. 3) high sensitivity to functional changes – studies have shown that functional connectivity 
(FC) measures are sensitive to changes in brain function, by showing that functional reorganization could 
be observed after as little as one week of intervention. Together, these advantages suggest that rsfMRI 
outcome measures, such as between-network connectivity (BNC; calculated as the degree of temporal 
dependency between functional networks) may be ideal for clinical observations and evaluation of the 
extent and pattern of cortical plasticity in SCI patients in response to therapeutic intervention. 
Here, we propose to examine functional organization within major brain networks of SCI patients 
using rsfMRI, and to assess the relationship between rsfMRI and clinical measures. In addition to 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 5 of 17 
 
development of a robust, clinically feasible rsfMRI data analysis pipeline, this study is expected to result in 
improved understanding of the functional reorganization that takes place during and after intervention. 
 
4. 
Study Procedures 
a. Study design, including the sequence and timing of study procedures   
(distinguish research procedures from those that are part of routine care). 
 
This will be an early phase 1 (phase 0) clinical trial. Specifically, the study will be performed as a 
randomized, parallel group trial to determine if the amount of changes in brain functional connectivity 
outcome measures (i.e., between network connectivity) is significantly different between the group of 
patients that perform FES cycling and another group of patients that perform passive (sham) cycling. 
 
Patients of the International Center for Spinal Cord Injury (ICSCI) at the Kennedy Krieger Institute 
(KKI) will be identified as meeting the inclusion criteria by reviewing the medical records held by the 
ICSCI. Once the patient consents by signing the consent form, official screening of subjects will be 
performed. Subjects will be randomized into 2 groups: FES cycling (Group 1; n=24) and passive cycling 
(Group 2; n=24). The patients will undergo either an FES cycling or a passive cycling sessions for 4 weeks, 
3 times a week. Acquisition of rsfMRI measures: MRI will be performed on all participants at the 
beginning (prior to cycling sessions) and at the end of the 2nd and 4th weeks of the intervention program. 
Acquisition of clinical measures: ISNCSCI and SCIM (Spinal Cord Independence Measure) evaluations 
will be performed to coincide with the dates of MRI acquisitions, to determine the neurological level and 
the degree of sensory and motor impairments. Detailed study timeline can be found in Figure 1. 
 
 
Figure 1. Study Timeline. 
 
 SCI patients assigned to FES cycling group will take part in the following evaluations: 
A: Medical chart review / MRI screening questionnaire 
B1: FES cycling trial 
C1: Neurological evaluation (ISNCSCI – more commonly known as ASIA exam) 
C2: Functional evaluation (SCIM) 
D: MRI 
 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
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E1: FES cycling 
 
 SCI patients assigned to passive cycling group will take part in the following evaluations: 
A: Medical chart review / MRI screening questionnaire 
B2: Passive cycling trial 
C1: Neurological evaluation (ISNCSCI – more commonly known as ASIA exam) 
C2: Functional evaluation (SCIM) 
D: MRI 
 
E2: passive cycling 
 
A: Medical chart review / MRI screening questionnaire 
 
For all subjects with spinal cord injury, their medical chart will be reviewed for the following information: 
 
Demographics 
Medical history (including labs) 
Physical history 
Neurological history 
Medication history 
Therapeutic plan 
Physical/occupational/aquatic therapy history (including outcome measures) 
 
This information is obtained as part of a routine care. The participant does not have to be physically present 
during this process. At this time, a standard MRI screening questionnaire will also be completed to be sure 
that it is safe for the participant to have an MRI exam. 
 
B: Cycling trial 
 
B1. FES cycling trial: This is a routine exam performed for people with spinal cord injury at the ICSCI. 
Once medically cleared to start an exercise program, subjects who are assigned to the FES cycling group 
will undergo a trial use of the FES cycle. This trial of FES will be overseen by a trained physical therapist 
experienced at setting up the FES cycle. The goal of this will be to ensure that the patient is willing and 
able to use the cycle. Participants who fail the FES trial will be excluded from the study. For additional 
details regarding the FES component, please see the E: Cycling section below. If the patient has 
successfully participated in an FES cycling program previously, this step will be omitted.  
 
B2. Passive cycling trial: This is a routine exam performed for people with spinal cord injury at the ICSCI. 
Once medically cleared to start an exercise program, subjects who are assigned to the passive cycling group 
will undergo a trial use of the FES cycle (but with the stimulation component OFF). This trial of passive 
cycling will be overseen by a trained physical therapist experienced at setting up the FES cycle. The goal of 
this will be to ensure that the patient is willing and able to use the cycle. Participants who fail the passive 
cycling trial will be excluded from the study. For additional details, please see the E: Cycling section 
below. If the patient has successfully participated in an FES cycling program previously (with or without 
the stimulation component), this step will be omitted.  
 
C: Neurological evaluation 
 
C1. American Spinal Injury Association (ASIA) Impairment Scale (ISNCSCI) evaluation: American 
Spinal Injury Association (ASIA) Impairment Scale (ISNCSCI) evaluation is part of a routine care 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 7 of 17 
 
evaluation performed for SCI patients at the International Center for Spinal Cord Injury (ICSCI) at 
Kennedy Krieger Institute. While its formal name is ISNCSCI, it is more commonly referred to as the 
ASIA exam. The evaluation consists of: 1) a motor component, where strength of ten key muscles (elbow 
flextors, wrist extensors, elbow extensors, finger flexors, finger abductors, hip flexors, knee extensors, 
ankle dorsiflexors, long toe extensors, and ankle plantar flexors) on each side of the body is evaluated, and 
2) a sensory component, where touch and pinprick sensations are tested on 28 dermatomes on each side of 
the body. The total evaluation time will not exceed 60 minutes. 
 
C2. Spinal Cord Independence Measure Version III (SCIM-III): The Spinal Cord Independence 
Measure Version III (SCIM-III) is a part of a routine care evaluation performed for individuals with SCI 
that assesses daily living and mobility activity performances. Specifically, it assesses the degree of self-care 
(feeding, grooming, bathing, and dressing), respiration and sphincter management, and mobility abilities 
(bed and transfers and indoors/outdoors). SCIM-III is frequently used in both clinical practice and clinical 
trial settings and is used to help guide clinicians in determining treatment goals and objectives for patients 
with an SCI. The SCIM takes approximately 30-45 mins to administer and score. However, the assessment 
will concurrently during the study participants' FES biking session, and will not contribute any additional 
time to the total study duration. 
 
D: Magnetic Resonance Imaging (MRI) 
 
This is a research procedure and not part of a routine care. All MR imaging will be performed at the F.M. 
Kirby Research Center using 3T scanners and consist of two main components: structural imaging of brain 
and spine, and functional imaging of brain and spine. Prior to imaging, an MRI technician will always 
perform an in-person safety screening, during which time any contraindications to MRI (e.g., aneurysm 
clips, pacemaker, etc.) will be identified. The total MR scan time will not exceed 90 minutes.  
 
Structural imaging of brain and spine: A structural MRI study of the spine and brain will be performed.  
The subject will be instructed to lie still during structural MRI sequences, and the subject will be permitted 
to sleep or to watch television projected onto a screen. 
 
Functional imaging of brain and spine: A functional MRI study of the spine and brain will be performed. 
The participants will be instructed to stay as still as possible with their eyes fixated on a cross hair on a 
screen.  
 
The MRI will be performed in a single visit, according to the participants’ convenience, tolerance, and 
availability. The neurological evaluation can be scheduled the same day as the MRI Imaging according to 
the subjects’ convenience, tolerance, and availability. 
 
E: Cycling 
 
By default, cycling activities will be conducted at KKI and supervised by a licensed physical therapist experienced at 
setting up the FES cycle. However, in response to the ongoing coronavirus pandemic and the recent surge of the 
omicron variant, and with an ultimate goal of minimizing risks to the study participants, if a study participant has their 
own FES cycle at home, the participant will be able to choose to conduct the FES cycling at home instead of at KKI. 
If the participant decides to pursue the at-home FES cycling, a licensed physical therapist will conduct a televisit, 
during which time the therapist will supervise and monitor the FES sessions via Zoom or Microsoft Teams.  
 
Once this protocol is approved, we will continue to offer online FES cycling sessions for study participants who prefer 
not to come for in-person visits. In order to maintain the consistency of FES cycling throughout the 4-week program, 
participants will not be able to switch between in-person and at-home FES cycling programs. The screening and MRI 
visits will still be conducted at KKI in person. All procedures listed below are routine practices in ICSCI. 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 8 of 17 
 
 
E1. Functional Electrical Stimulation cycling: The FES cycling group (Group 1) will use RT300 
ergometer (Restorative Therapies, Inc., Baltimore, Maryland). The RT300 ergometers are currently 
installed at ICSCI according to Kennedy Krieger Institute and Johns Hopkins Hospital safety guidelines. 
The muscles chosen for stimulation will be the bilateral glutei, quadriceps and hamstrings. The FES 
stimulation parameters will be set as follows: waveform biphasic, charged balanced; phase duration 
typically of 250 microseconds; pulse rate 33 to 45 pulses per sec (pps). The stimulus intensity of each 
channel will be adjusted for individual patients and muscle group so that a tolerable stimulation is provided 
that will generate a cycling action (0-140 mA). Target cycling speed is 50 RPM. Resistance will be 
automatically adjusted by the FES bike according to the subject’s performance. When fatigue occurs, 
participants will continue cycling with electrical stimulation and motor support. FES therapy will be 
administered for one hour per session 3 times a week. 
 
E2. Passive cycling: The passive cycling group (Group 2) will use the same RTI 300 ergometer however 
during this period stimulation will not be turned on. Instead, continuous motor support will be activated 
resulting in passive cycling. Target cycling speed is 50 RPM. Participants assigned to passive cycling will 
be required to have one hour of passive therapy 3 times a week for the entire duration of treatment 
assignment. 
 
b. Study duration and number of study visits required of research participants. 
 
Patients will be evaluated for appropriateness of enrollment and informed consent will be obtained.  During 
the next 8 weeks, the screening process will be completed. A trial of FES will be performed at Kennedy 
Krieger Institute ICSCI to ensure that the participant is able to tolerate the stimulations of this exercise 
modality. If he or she is willing and able to proceed with the study then baseline data will be obtained at the 
beginning of week 1. The detailed study timeline can be found in Figure 1. The study duration for each 
assessment is as follows: 
 
A: Medical chart review: N/A 
B: FES/passive cycling trial (30 min) 
C1: Neurological evaluation (up to 1 hour, part of routine care in ICSCI; total of 3 times over 4 
weeks) 
C2: Functional evaluation (up to 45 min, part of routine care in ICSCI; total of 3 times over 4 
weeks; to be performed simultaneously during one of E1 or E2 sessions) 
D: MRI (up to 90 minutes; total of 3 times over 4 weeks) 
E1: FES cycling (1 hour, 3 times a week) 
E2: Passive cycling (1 hour, 3 times a week) 
 
We expect to enroll an average of 4 subjects each month into the trial with a total number of subjects 
of 48 (24 per group). Since participants will be enrolled in the study for 4 weeks, then the entire duration of 
the study will be around 1.5 years. After completing 24 subjects enrollment will be paused for interim 
analysis when it will be decided whether enrollment will continue. 
 
c. Blinding, including justification for blinding or not blinding the trial, if applicable. 
 
Because of the nature of the interventions (i.e., electrical stimulation), study participants cannot be 
completely blinded to the treatment they will receive. This is because many participants will have a residual 
motor and sensory functions and ‘feel’ which intervention they are receiving. Therefore, this study will be 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 9 of 17 
 
performed as a single-blinded randomized trial. Study physicians and research staff who perform study 
measurements on participants will be blinded from the intervention the study participants receive. 
 
d. Justification of why participants will not receive routine care or will have current therapy 
stopped. 
 
All participants will receive routine care for treatment of spinal cord injury. Participants will not be asked 
to stop their current medications or therapy. All subjects will continue to consistently perform their usual 
(“baseline”) amount of physical activity throughout the study, including home exercise stretching program, 
cardiovascular conditioning, etc. “Baseline” activity is defined as amount of physical activity performed for 
at least 1 month prior to enrollment. Routine care will not be interrupted. 
 
e. Justification for inclusion of a placebo or non-treatment group. 
 
Patients who are assigned to the passive cycling group will act as a non-treatment group. By comparing the 
outcome measures of the FES- and Passive-cycling groups, we will be able to determine whether it is the 
active neuromuscular conduction triggered by FES that leads to alteration in cortical functional 
connectivity, as opposed to a simple movement of muscles. Physiological effects of FES cycling require 
treatment for several months. Our proposed study is short (4 weeks). And as such, we expect minimal 
neurological differences between the FES and passive cycling groups. In contrast, we expect early, 
observable, and detectable differences in cortical functional connectivity between the FES and passive 
cycling groups. 
 
f. Definition of treatment failure or participant removal criteria. 
 
Subjects may withdraw from the study at any time for any reason. Additionally, a subject may be removed 
from the study for any of the following reasons: 
 The subject experiences a medical emergency that necessitates discontinuation of therapy 
 The subject experiences a serious adverse event that is judged to be likely related to the assigned 
treatment group or is of severity that warrants discontinuation of assigned treatment. 
 For any medical reason at the discretion of the investigator. 
 Subject is not compliant: participants who miss more than 3 sessions of cycling for the duration of 
the study. 
 Subject becomes pregnant. 
 
g. Description of what happens to participants receiving therapy when study ends or if a 
participant’s participation in the study ends prematurely. 
 
Upon completion of the study, participants will be referred back to their treating SCI specialist who will be 
made aware of the treatment and follow-up.  The same protocol will be followed for patients who terminate 
the study early.  In the event of discontinuation due to adverse event, participants will be followed by the PI 
and a medical supervisor of the study (Dr. Sadowsky) until resolution or stabilization of their adverse 
condition and then referred back to their treating SCI specialist. 
 
5. 
Inclusion/Exclusion Criteria 
 
Only subjects who agree voluntarily to participate in these procedures after they have been fully informed 
will be included, and who can comprehend the nature of these procedures can participate. Also, their actual 
involvement will be discussed with them repeatedly to assure adequate knowledge. Subjects will be 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
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Page 10 of 17 
 
included only if one can understand the nature of the experiment as presented in English, and can cooperate 
with symptom assessment in English. 48 subjects will be recruited in total over a period of two years. 
 
Inclusion criteria: 
 Adult (18-99 years) men and women of all ethnic groups 
 SCI, traumatic  
 Thoracic (T1-T12) and lumbar (L1, L2), without the involvement of lower motor neurons. 
 ASIA classification A-D 
 Chronic injury: > 6 months from the injury 
 Satisfactory general health  
 No FES ergometer (i.e. RT300 or equivalent) use within 4 weeks. 
 Ability to comply with procedures and follow-up 
 
Exclusion criteria: 
 Contra-indication to MR study (e.g., cardiac pacemaker, claustrophobia, aneurysm clip, etc.) 
 History or clinical evidence of moderate or severe brain injury 
 Major spine deformity (e.g. scoliosis, kyphosis, subluxation) 
 Movement disorder or severe spasticity preventing ability to lay still for extended periods required 
for imaging. 
 Women who are pregnant  
 Concurrent lower motor neuron disease such as peripheral neuropathy that would exclude lower 
extremity electrical excitability 
 Unstable long bone fractures of the lower extremities. 
 Subjects with history of inability to tolerate electrical stimulation. 
 
Pregnancy is associated with significant physiological deviations with respect to cerebral spinal fluid 
dynamics and blood flow in the middle cerebral artery that are different than what is seen in women who 
are not pregnant.  Gonadal steroids associated with pregnancy are also implicated in marked changes in 
cognitive function. Because of the significant changes from the normal, non-pregnant condition it is 
important to exclude pregnant women from many studies. If they were not excluded their data would 
significantly add to the variance of the physiological and behavioral measures. Furthermore, that variance 
is not readily interpreted at this time. 
 
6. 
Drugs/ Substances/ Devices 
a. The rationale for choosing the drug and dose or for choosing the device to be used. 
 
The RT-300 FES bike has been FDA-cleared for use in general rehabilitation (the device clearance number 
is K072398).  It has been a standard rehabilitation treatment modality at our center for several years. 
 
b. Justification and safety information if FDA approved drugs will be administered for non-FDA 
approved indications or if doses or routes of administration or participant populations are 
changed. 
 
N/A 
 
c. Justification and safety information if non-FDA approved drugs without an IND will be 
administered.  
 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
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Page 11 of 17 
 
N/A 
 
7. 
Study Statistics 
a. Primary outcome variable. 
 
Type
Name
Time Frame
Brief Description
Primary
International 
Standard of 
Neurological 
Classification for 
Spinal Cord Injury 
(ISNCSCI) 
baseline, mid-
intervention, 
post-
intervention 
Developed by the American Spinal Injury 
Association (ASIA) as a universal classification 
tool for spinal cord injury (SCI). The 
classification tool involves a sensory and motor 
examination to determine the neurological level 
of the injury and whether the injury is complete 
or incomplete. The tool also provides sensory 
and motor scores of upper and lower body, as 
well as right and left of the body. The ISNCSCI 
defines neurological level as the most caudal 
level at which sensory and motor function are 
intact. The completeness of the injury is graded 
according to the ASIA Impairment Scale 
(ISNCSCI).
Primary
Resting state fMRI 
functional 
connectivity 
Baseline, mid-
intervention, 
post-
intervention 
RsfMRI functional connectivity is defined as the 
temporal dependency of neuronal activation 
patterns (represented by the blood oxygenation 
level dependent (BOLD) signal time courses as 
measured using rsfMRI) of anatomically 
separated brain regions. There are number of 
methodologies one can use to characterize the 
degree and type of rsfMRI functional 
connectivity. One example is between-network-
connectivity (BNC), which is defined as the 
degree of correlation between two time courses 
obtained from a pair of brain regions. Summary 
statistics of BNC (e.g., mean, variance), as well 
as the dynamic properties of BNC (e.g., dynamic 
functional connectivity) can be used to further 
summarize the characteristics of the functional 
connectivity in SCI population.
Primary
RsfMRI brain parcels Baseline, mid-
intervention, 
post-
intervention 
RsfMRI functional connectivity can also be used 
to identify functionally homogeneous brain 
regions, or parcels of the brain. The parcels' 
center of mass, spatial maps, average and 
variance of the BOLD signal time courses within 
the parcels can be used to characterize brain 
functional organization.
 
b. Secondary outcome variables. 
 
Type
Name
Time Frame
Brief Description

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 12 of 17 
 
Secondary
FES cycling 
parameters 
During 
intervention 
The degree of electrical stimulation is adjusted 
specifically for each patients, depending on the 
patients level of sensory and motor impairment, as 
well as the patient's level of tolerance for sensation and 
fatigue. Accordingly, the strength and frequency of the 
electrical stimulation applied during each FES cycling 
session will be recorded. The duration of the cycling 
session performed will also be recorded. These 
parameters may be used as higher-order confounds 
during statistical data analysis
Secondary
Passive 
cycling 
parameters 
During 
intervention 
The amount of time and the degree of resistance used 
by the patients during the passive cycling sessions will 
be recorded, and may be used as higher-order 
confounds during statistical data analysis.
Secondary
Personal 
information 
Baseline 
Patient's age, sex, handedness, and time since injury 
will be recorded, and may be used as higher-order 
confounds during statistical data analysis.
Secondary
SCIM 
baseline, mid-
intervention, 
post-
intervention 
The Spinal Cord Independence Measure Version III 
(SCIM-III) assesses daily living and mobility activity 
performances. Specifically, it assesses the degree of 
self-care (feeding, grooming, bathing, and dressing), 
respiration and sphincter management, and mobility 
abilities (bed and transfers and indoors/outdoors) and 
each category are scored using the SCIM 
questionnaire. SCIM-III is frequently used in both 
clinical practice and clinical trial settings and is used 
to help guide clinicians in determining treatment goals 
and objectives for patients with an SCI.
 
c. Statistical plan including sample size justification and interim data analysis. 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 13 of 17 
 
 
Preliminary study: In this preliminary study, we hypothesized that BNC of sensorimotor and visual 
networks will correlate with the total ISNCSCI score, and performed the study to determine the feasibility 
of a larger population study. Twelve SCI patients were recruited, and the relationship between the 
ISNCSCI score and BNC measurements was examined. ISNCSCI sub-scores were first obtained, which 
were: total upper and lower body motor scores, and total sensory score. The sum of the three scores 
provided the total ISNCSCI scores. Analysis of the data consisted of preprocessing, PCA, and GICA, and 
total of 14 intrinsic functional components were identified. BNC between the sensorimotor and visual 
networks were computed, and plotted against the total ISNCSCI scores. Linear regression analysis was 
performed to find the best linear fit for the plots. Stronger BNC between the sensorimotor and visual 
networks was associated with lower total ISNCSCI scores (R2=0.35, p = 0.04; Figure 2Figure 2). In other 
words, patients with greater degree of physical impairment tended to have stronger functional connectivity 
between the sensorimotor and visual networks, suggesting compensatory plastic cortical changes that are 
related to clinical presentation of the patients. Overall, BNC measures showed good correlations with the 
total ISNCSCI scores, supporting our hypothesis.  
Between network connectivity (BNC) measurements from the above preliminary study provided 
means, standard deviations, and correlation coefficients for 12 SCI patients. A power analysis1 revealed 
that a sample size of 24 subjects will be required to achieve 80% power at an alpha of 0.018; the alpha level 
was lowered with the correction for multiple comparisons in mind. We will therefore recruit a total of 48 
patients. At this point, we do not have enough information about the variability of the BNC in response to 
the FES to perform a more stringent power analysis. We will 
use the data in the first 24 SCI subjects recruited to the study 
to assess the degree of variability in the metric. Based upon 
these estimates, we will then perform a power analysis to 
determine how many more subjects will need to be enrolled 
to assess the significance of our findings. 
The spatial maps of ICA- and SCA-derived brain 
parcels will be compared across groups. First, the 
participant-specific sensory and motor brain parcels will be 
converted to z values, so image intensities reflect the degree 
to which the parcel is present in each participant’s data. The 
brain parcels will be combined in a second-level random 
effects analysis using a two sample t-test in SPM8. Voxels 
that contributed unequally to the parcels across groups will 
be identified using a liberal voxel-wise p value of 0.01 and a 
cluster-level p value of 0.05 corrected for multiple 
comparisons2. The between network connectivity (BNC) 
between sensory and motor parcels will be calculated using 
Pearson’s correlation coefficient between pairs of participant 
specific motor and sensory brain parcels3. Pairwise-
correlations will be converted to Z-scores using Fisher’s transformation, and the BNC across groups will be 
compared using two-sample t tests and adjusted p-values using a false discovery rate correction. Next, we 
will investigate whether sensory and motor BNC measured at week 2 of cycling program are related to 
motor and sensory International Standards for Neurological Classification of Spinal Cord Injury (ISNCSCI) 
scores measured at week 4, using a multivariate linear regression model analysis. Finally, the longitudinal 
inter- and intra-subject reproducibility of the ICA- and SCA-derived brain parcels will be asses using intra-
class correlation coefficient (ICC). 
 
d. Early stopping rules. 
Figure 2. Correlations between 
sensorimotor-visual BNC measurements 
and total ISNCSCI scores in SCI patients 
suggest a compensatory plastic cortical 
changes that are related to clinical 
presentation of the patients. Patients with 
lower ISNCSCI score showed larger degree 
of functional connectivity between the 
sensorimotor and visual networks.

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 14 of 17 
 
 
The principal investigator may discontinue the study if the interim statistical analysis as described above 
indicates that the number of subjects required for this trial exceeds 50.  
 
Patients may withdraw from the study at any time for any reason.  Any investigator may discontinue a 
patient for any of the following reasons: 
 The subject experiences a medical emergency that necessitates discontinuation of therapy 
 The subject experiences a serious adverse event (WHO Grade IV-V adverse events) that is judged 
to be likely related to the assigned treatment group or is of severity that warrants discontinuation of 
assigned treatment. 
 For any medical reason at the discretion of the investigator. 
 
Individual participants will be removed from the study if they experience toxicity or complications as 
described above.  
 Fails to follow directions. 
 Are not compliant: participants who miss more than 3 sessions of cycling for the duration of the 
study. 
 Unwilling to perform the second lumbar puncture prior at the end of the study. 
 Become pregnant. 
 
8. 
Risks 
a. Medical risks, listing all procedures, their major and minor risks and expected frequency. 
 
The medical risks are defined in the section below (‘Steps taken to minimize the risks’).  This allows 
combining the risk and risk management in the same section for each risk. 
 
b. Steps taken to minimize the risks. 
 
A: Medical chart review / MRI screening questionnaire 
 
Aside from the risk associated with disclosing personnel or protected health information outside the 
research study and possible discomfort with being asked personal questions, there are no known risks 
associated with this measurement. 
 
B: FES trial & E: Cycling 
 
The risk associated with FES is pain at the stimulation site.  To minimize the risk, stimulation will only be 
done to the participant’s tolerance level.  There is a minimal risk of skin burn.  To further minimize the risk 
of skin burn, only appropriate size electrodes will be used and they will replaced as per the manufacturer’s 
recommendations. 
 
The safety of FES for use during pregnancy has not been established. Therefore, pregnant women will 
not be enrolled in the study.  To minimize the risk, any females who are of child bearing age will be asked 
to undergo pregnancy testing prior to the start of the study as well as agree to use an effective method of 
contraception during the study. 
 
C: Neurological and Functional evaluation 
 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 15 of 17 
 
There is a risk of discomfort at the site of the pin prick during the ISNCSCI evaluation.  To minimize the 
risk, only the professionally trained personnel at the ICSCI will perform the ISNCSCI evaluation. 
 
The risks associated with functional evaluation (SCIM) are extremely low. The tasks could cause boredom 
or maybe distracting for some participants. To minimize the risk, study participants will be informed that 
they are free to take breaks while answering the questionnaire as often as necessary. 
 
D: MRI 
 
The risks associated with magnetic resonance imaging are extremely low. They include the possibility that 
undetected metal in the subject’s body could be displaced by the magnetic field of the MRI scanner. 
Participants could become claustrophobic while in the scanner. Participants could experience discomfort in 
attempting to remain still for up to 90 minutes in the scanner. The tasks could cause boredom or anxiety in 
some participants. Credit cards, watches, or other items could be damaged by the magnetic field if they are 
inadvertently brought into the scan room. Some volunteers may experience dizziness when being in the 
scanner. Head phones and ear-plugs are provided to the subjects to protect subjects from scanner gradient 
noise. To minimize risk, following measures will be taken: 
 All subjects are screened for contra-indications for magnetic resonance, namely severe 
claustrophobia, pregnancy, cardiac pacemaker, orthodontics (braces) or other non-MR compatible 
ferromagnetic implant. In addition, access to the scan room is strictly controlled to ensure that no 
ferromagnetic materials are introduced. The scanners to be used in these studies are FDA approved 
and operates under radiofrequency power monitoring software at all times. All scan procedures at 
magnetic field strengths of 3T are FDA approved and are not classified as investigational devices.  
 The subjects have the option of terminating the testing at any time without penalty if they so 
choose. The risks of psychological discomfort will be minimized by encouraging subjects to let the 
examiner know if they are feeling any discomfort, and by continuous monitoring by experienced 
operators for subject fatigue, inattention, or annoyance. Scanning will be halted if the subject so 
requests, or if the examiner feels that the subject is becoming uncomfortable. The subject will be 
encouraged to report any adverse symptoms during the MRI. The MRI can be stopped by the 
subject either by verbalizing the request to stop (which can be heard through the microphone in the 
MRI) or by pushing a “panic button” provided. 
 A potential concern with MRI studies is so-called radiofrequency heating due to radiofrequency 
power deposition in the subject. The FDA has set strict and very conservative guidelines to guard 
against this risk. Such power deposition increases with the square of the magnetic field strength. 
However, it is possible to stay within these guidelines. To be 100% sure of compliance with the 
FDA guidelines, power deposition is monitored continuously by the software of the manufacturers 
and scans are not possible if the power deposition would exceed guidelines. 
 This study includes operator-controlled changes to the pattern and timing of an MRI signal or pulse 
sequence that varies from the standard sequences used by the MRI manufacturer at lower field 
strengths. These changes will operate within FDA guidelines. 
 
Other risks: Time commitment 
 
The time commitment required to complete all study over 4 weeks may be inconvenient. To minimize this 
risk, the participant: 1) will be instructed to contact the study coordinator if the participant is having 
problems scheduling study visits, or adhering to scheduled study visits ahead of time; 2) will be excluded 
from the study if the participant cannot commit the time and effort to the study; 3) will be told that the start 
of the study will be arranged in such a way that it reduces any disruption to the participant’s social, work or 
school commitments. 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 16 of 17 
 
 
c. Plan for reporting unanticipated problems or study deviations. 
 
During this study, medical history and physical examination will be performed at baseline and at regular 
intervals for measurement of residual sensorimotor functions in patients with spinal cord injury. All of the 
materials collected are for research purposes only, and data will be kept in strict confidence. No 
information will be given to anyone without permission from the subject. The consent form includes the 
informed consent statement required by Johns Hopkins University School of Medicine for studies involving 
human subjects. This statement guarantees confidentiality, which will be ensured by use of identification 
codes. All data, whether generated in the laboratory or at the bedside, will be identified with a randomly 
generated identification code unique to the subject. 
The Principal Investigator (PI) will be responsible for ensuring participants’ safety on a daily basis. 
The PI will also monitor participant safety, evaluate the progress of the study, to review procedures for 
maintaining the confidentiality of data, the quality of data collection, management, and analyses. Dr. 
Cristina Sadowsky, M.D., is the Clinical Director of the International Center for Spinal Cord Injury 
(ICSCI), and she will aid the PI in her capacity as a clinical mentor of the study in monitoring the study’s 
participants’ safety. 
Adverse events (AE), unanticipated problems and/or study deviations will be reported in writing by the 
PI to the Johns Hopkins Medical Institute-IRB and Kennedy Krieger Institute Office of Research 
Compliance within 24 hours of notification. AE reports and annual summaries will not include subject- or 
group-identifiable material. Each report will only include the identification code. Twice annually, the PI 
will review study progress, data quality, and participants safety and share the reports with other study 
members of the group. 
All research material will be kept confidential and any means of subject identification (name and history 
number) will be removed from all material for analysis or presentation. No identifying information will be 
made publicly available. In some cases, individual scans will be included in published papers or meeting 
papers or posters, but the identity of the subject in question will not be revealed. There are minimal legal 
risks associated with breach of confidentiality for this study.  To minimize the risk of breach of 
confidentiality, access to participant/study data will be limited to study team members only.  All study data 
will be stored in a department al locked cabinet and secure database program. 
 
d. Legal risks such as the risks that would be associated with breach of confidentiality. 
 
There are minimal legal risks associated with breach of confidentiality for this study. To minimize the risk 
of breach of confidentiality, access to participant/study data will be limited to study team members only. 
All study data will be stored in a department al locked cabinet and secure database program. Additionally, 
all research material will be kept confidential and any means of subject identification (name and history 
number) will be removed from all material for analysis or presentation. No identifying information will be 
made publicly available. In some cases, individual scans will be included in published papers or meeting 
papers or posters, but the identity of the subject in question will not be revealed. 
 
e. Financial risks to the participants. 
 
There are no financial risks to participants for any of the study tests.  There will be no cost to the 
participant or the participant’s insurance company for the MRI scans done specifically for this study. The 
scans will be paid by funds from this grant application. Subjects will be responsible for the cost of travel to 
and from the Institute, as well as any food/meals purchased throughout the day while engaged in study 
procedures.  Valet parking is available at no cost. 
 

Date: 4.14.2023 
Principal Investigator: Ann S. Choe, Ph.D.  
Application Number: IRB000182576 
JHMIRB eFormA  01 
Version 3 Dated:   06/2007 
 
Page 17 of 17 
 
9. 
Benefits 
a. 
Description of the probable benefits for the participant and for society. 
 
Individual subject: There is no direct benefit to the individual subject, except that the MRI report they 
receive may contain information useful to their physicians. 
 
Society: Once developed and validated, the proposed MRI measures may yield surrogate biomarkers of 
treatment and/or rehabilitation therapy responses in SCI patients for use in clinical trials and drug 
discovery. Additionally, the developed methods may have broader implications in a number of other 
movement disorders (e.g., stroke and Parkinson’s disease). 
 
10. 
Payment and Remuneration 
a. 
Detail compensation for participants including possible total compensation, proposed bonus, 
and any proposed reductions or penalties for not completing the protocol. 
 
After completing the study, participants will receive a total of $525 compensation for their contribution. 
The costs for each visit are as follows: 
 MRI visits: 3 sessions at $25 per session, totaling $75. 
 ASIA visits: 3 sessions at $50 per session, totaling $150. 
 FES visits: 12 sessions at $25 per session, totaling $300.  
Compensation will be provided via a check, and participants will receive a structural images of their brain 
as a souvenir. 
 
11. 
Costs 
a. 
Detail costs of study procedure(s) or drug (s) or substance(s) to participants and identify 
who will pay for them. 
 
There is no cost to study participants for any of the study tests.  Subjects will be responsible for the cost of 
travel to and from the Kennedy Krieger Institute (Valet parking is available at no cost to study participant), 
as well as any food/meals purchased throughout the day while engaged in study procedures.