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General Questions

I would like to start a new project. What should I do?
To start you must fill the reception form and send it to CRM@nbml.ir, New NBML projects can be submitted through mechanisms that will be determined by the responsible committee, then we call you .
Can I get free or discounted scans for technical development?
yes, there are some forms , such as:
• MRI New Project Checklist .
• TMS New Project Checklist .
• TDCS New Project Checklist.
• FNIRS New Project Checklist.
• EEG New Project Checklist.
Can I get free or discounted scans for technical development?
No. If pre-production scan time is needed for testing of protocols, etc. You may apply for pilot project that involves technical development, but pilot studies are not "free" or "discounted" scans.
How will I get the data that I collect on the MRI or … scanner into my laboratory for analysis?
1. Burn the data onto a CD/DVD during your scanning session.
2. Transfer the data electronically to a designated server which you can then access the data.
What provisions are available for data processing and display in the NBML?
Several computers are available in the user's computer room.

tES Section

What is tES (Transcranial Electrical Stimulation)?
Transcranial Electrical Stimulation is a non-invasive stimulation which applies a 1-2mA direct electrical current between anodal and cathodal electrodes to make excitation or inhibition in subsequent brain regions. Different electrode montages are used in various brain regions, and simulation of input and output electrical current helps to improve montage and affects cognition and disease.
What does electrode montage mean?
It’s determining and positioning electrodes on the brain regions, shoulder and arm to make the desired function and electrical current path. For each treatment and cognitive assessment, there are different electrode positioning.
What facilities can be found in tES laboratory?
tES facilities are explained in Services and equipment section on our webpage, in detail. https://nbml.ir/EN/services/tDCS-Lab
Which parameters are required for a tES session?
In direct current stimulation, running a session require information of anode, cathode and reference (if it is needed) electrode position, current intensity, stimulation duration, ramp up and ramp down times. In alternative current stimulation current frequency and phase are needed in addition.
What is tES and TMS differences?
In TMS there is a magnetic field in the coil which induces an electrical current and field in 0.5 cm2 and about 2cm depth on the brain and can cause cortex activity, e.g., stimulating motor cortex causes muscle activation. In tES a small direct electrical current is used on 1 to 35 cm2 (each electrode) brain region to make effects.

EEG Section

What is Electroencephalography?
Electroencephalography (EEG) is a non-invasive technique for measurement of the electrical activity of the brain; EEG has a high temporal resolution compared to other brain mapping techniques.
What types of studies can be performed using Electroencephalography?
Electroencephalography can be used as a tool to evaluate and model brain function during cognitive tasks. Besides, evaluation of medical interventions effects such as (transcranial electrical/magnetic stimulation, medication, and therapeutic consultation) is achievable with pre/post electroencephalography. For more information, please visit the service section on our webpage.
What sorts of stimulus can be presented to the participants?
We can measure the individual’s response to visual, auditory, somatosensory (vibration, electrical) stimuli.
What are the lab equipment for data recording?
The lab is equipped with
- (64+16) 80 channel amplifier g.HIamp (g.tec)
- 32 channel amplifier g.USBamp (g.tec)
- 32 channel EEG cap g.Nautilus (g.tec)
- (64+16) 80 channel MR-compatible amplifier BrainAmp MR Plus (Brain Product)
- Set of sensors for physiological parameters recording
What are the approaches for stimuli presentation?
It’s recommended to use common toolboxes such as Psychtoolbox & Cogent to implement various cognitive tasks. Use of any programs or scripts written in other programming languages than MATLAB is approved.
What are the approaches for stimuli presentation?
Three main approaches can be taken to send synchronization triggers to the digital input of an amplifier?
1- Sending triggers to the parallel port on the stimulation PC. (Click to receive the sample code for parallel port handling)
2- Using optical sensors that are sensitive to changes in illumination intensity. (If you put these sensors on a point on the presentation screen that would change simultaneously with an important event in your tasks such as stimulus presentation or user’s response you will have the time tags on your EEG data.
3- Using Push buttons to mark any desired time points in your data.
What information is achievable at each session?
Each session, the lab provides you with the recorded signals and synchronization triggers in a single file with .mat format that can be loaded in MATLAB easily.
Are the electrode coordinates on subject’s head available?
In case you can receive the approximate electrode coordinates from our lab specialist. Also, there is an opportunity to extract the precise electrode locations using the Navigation system available in the TMS lab.

TMS Section

What is repetitive Transcranial Magnetic Stimulation (rTMS)?
rTMS is an effective, non-invasive alternative for the large number of patients not responding to medication. rTMS does not require anesthesia – and is not to be confused with ECT (Electro Convulsive Therapy). The rTMS system delivers magnetic pulses to stimulate nerve cells in the part of the brain controlling the mood. The rapid change in the magnetic field induces a current, and if the current induced is of sufficient amplitude and duration, it will excite neurons.
What are the side-effects of rTMS?
rTMS is well-tolerated and associated with few side-effects and only a small percentage of patients discontinue treatment because of these. The most common side-effect, which is reported in about half of patients treated with rTMS, is headaches. These are mild and generally diminish over the course of the treatment. Over-the-counter pain medication can be used to treat these headaches.
About one third of patients may experience painful scalp sensations or facial twitching with rTMS pulses. These too tend to diminish over the course of treatment although adjustments can be made immediately in coil positioning and stimulation settings to reduce discomfort.
The rTMS machine produces a loud noise and because of this earplugs are given to the patient to use during the treatment. However, some patients may still complain of hearing problems immediately following treatment. No evidence suggests these effects are permanent if earplugs are worn during the treatment.
rTMS has not been associated with many of the side-effects caused by antidepressant medications, such as gastrointestinal upset, dry mouth, sexual dysfunction, weight gain, or sedation.
The most serious risk of rTMS is seizures. However, the risk of a seizure is exceedingly low. At Johns Hopkins, we follow up-to-date safety guidelines that are designed to minimize the risk of seizures. While rTMS is a safe procedure, it is important to point out that because it is a new treatment, there may be unforeseeable risks that are not currently recognized.
Who cannot get rTMS?
Patients with any type of non-removable metal in their heads (with the exception of braces or dental fillings), or within twelve inches of the coil should not receive rTMS. Failure to follow this rule could cause the object to heat up, move, or malfunction, and result in serious injury or death. The following is a list of metal implants that can prevent a patient from receiving rTMS:
• Aneurysm clips or coils
• Stents in the neck or brain
• Implanted stimulators
• Cardiac pacemakers or implantable cardioverter defibrillator (ICD)
• Electrodes to monitor brain activity
• Metallic implants in your ears and eyes
• Shrapnel or bullet fragments in or near the head
• Facial tattoos with metallic or magnetic-sensitive ink
• Other metal devices or object implanted in or near the head
Is TMS Therapy uncomfortable?
No, the most common side effect related to treatment was scalp discomfort during treatment sessions. This side effect was generally mild to moderate, and occurred less frequently after the first week of treatment.
If necessary, you can treat this discomfort with an over-the-counter analgesic. If these side effects persist, your doctor can temporarily reduce the strength of the magnetic field pulses being administered in order to make treatment more comfortable.
Less than 5% of patients treated with TMS Therapy system discontinued treatment due to side effects.
What happens during an rTMS procedure?
For each rTMS session, the patient sits in a specially designed treatment chair, much like the kind used in a dentist’s office. Because rTMS uses magnetic pulses, before beginning a treatment, patients are asked to remove any magnetic-sensitive objects (such as jewelry, credit cards). Patients are required to wear earplugs during treatment for their comfort and hearing protection, as rTMS produces a loud clicking sound with each pulse, much like an MRI machine.
During the first rTMS session, several measurements are made to ensure that the TMS coil will be properly positioned over the patient’s head. Once this is done, the TMS coil is suspended over the patient’s scalp. The TMS physician then measures the patient’s motor threshold, by administering several brief pulses. The motor threshold is the minimum amount of power necessary to make the patient’s thumb twitch, and varies from individual to individual. Measuring the motor threshold helps the physician personalize the treatment settings and determine the amount of energy required to stimulate brain cells.
Once the motor threshold is determined, the coil is then brought forward so that it rests above the front region of the patient’s brain. Treatment is then commenced. During the treatment, patients will hear a series of clicking sounds and will feel a tapping sensation under the treatment coil.
Succeeding treatment sessions do not require that the motor threshold be determined again, unless indicated otherwise, such as when changes in medications are made during the course of the treatment.
Which parameters is needed for an rTMS session?
For an rTMS session researcher should determine waveform, coil type, coil positioning on brain, intensity in %Motor threshold, frequency, pulse number in each train or train duration, inter-train interval, total number of train according to safety articles.
What does it mean by EMG signal during TMS evaluation?
We can detect the MEP response of a specific brain area by TMS pulse. The MEP detected with surface electromyography (EMG) quantifies the level of the corticospinal tract and corticobulbar tract excitability (spatially in neurological disorders). For example, when TMS is applied over M1, it can elicit contraction in contralateral muscles.
What are the facilities available for EMG acquisition during TMS?
There are 3 EMG acquisition systems for concurrent TMS-EMG such as:
• Magventure EMG system
• Motion Lab EMG system
• Wireless and wired Bayamed EMG system
Is EMG signal analysis service available in NBML?
Yes, we provide EMG signal analysis service in NBML.
What kind of results is accessible after data acquisition session?
You will be provided by the EMG output files in the .xlsx or .txt formats as well as motor thresholds.
Would you adjust the EMG system parameters such as sampling frequency and … as my research design?
Yes, we can adjust EMG system parameters as you want such as sampling frequency, number of channels, bandwidth, magnification and ….

fNIRS Section

What is functional Near-Infrared Spectroscopy?
functional Near-Infrared Spectroscopy (fNIRS) is a non-invasive technique for measurement of the hemodynamic response that monitors the relative changes in the concentrations of (de)oxyhemoglobin.
What types of studies can be performed using functional Near-Infrared Spectroscopy?
functional Near-Infrared Spectroscopy can be used as a tool to evaluate and model brain function during cognitive tasks. Besides, evaluation of medical interventions effects such as (transcranial electrical/magnetic stimulation, medication, and therapeutic consultation) is achievable with pre/post functional Near-Infrared Spectroscopy. For more information, please visit the service section on our webpage.
Is it possible to use functional Near-Infrared Spectroscopy with other modalities simultaneously?
In this lab, we can record fNIRS simultaneously with all other modalities including functional Magnetic Resonance Imaging (fMRI), Electroencephalography (EEG), Transcranial Electrical Stimulation (TES), Transcranial Magnetic Stimulation (TMS), Virtual Reality (VR) and Eye-tracking.
What sorts of stimulus can be presented to the participants?
We can measure the individual’s response to visual, auditory, somatosensory (electrical) stimuli.
What are the lab equipment for data recording?
The lab is equipped with the 48-channel device with MR-compatible fiber optics
• What are the approaches for stimuli presentation?
It’s recommended to use common toolboxes such as psychtoolbox & Cogent to implement various cognitive tasks. Use of any program or script written in other programming languages than Matlab is approved.
What is the approach for stimuli presentation?
Sending triggers through parallel port on stimulation PC is the way to synchronize task flow and data recording.
What information is achievable at each session?
Each session, the lab provides you with the recorded signals and synchronization triggers in a single file with .xls , .oxy3, .xml.
Where can we get the electrode coordinates?
In case you can receive the approximate optode coordinates from our lab specialist. Also, there is an opportunity to extract the precise optode location using the Navigation system available in the TMS lab.

MRI Section

Can I save raw” TWIX” or “.rda” data for spectroscopy?
Yes, raw data can be exported and saved to a temporary network account folder.

• TWIX data must be saved immediately after the scan session.

• .rda can be exported and saved at any point while the scan is still on the scanner console computer.

2. What will be the file format of the MRI data that I collect?
The Siemens MR scanners use DICOM as their native file format and this format must be used for CD's burned from the console.
The pre-built Siemens fMRI protocols seem to want to know details about the stimulation protocol (on-off periods, etc). Is it really necessary to provide these details to acquire data?
No. The stimulation protocol information is used to create t-test images as part of automatic data processing. This assumes a simple on-off protocol. You can use this feature if you want, but its validity should have no impact on the raw data that you collect. When appropriate, you may find t-test image helpful in providing an early look at your data (e.g., in deciding whether a pre-surgical fMRI study is of good quality).
The scanners want to save fMRI data with the entire volume "mosaicked" onto a single plane. I can't process data in this format. What can I do?
Most fMRI processing software that reads native DICOM data is now able to handle Siemens mosaic data. The scanner software does include an option for reversing this "mosaicked" process. However, this will create an enormous number of files since each slice is saved as a separate file.
How would we go about installing new devices in the scanner environment (e.g. response boxes, custom head restraints, etc)?
All electrical equipment needs to be reviewed to assure that it is implemented in a way that does not introduce electrical noise into the scanner environment. All objects to be brought into the scanner room must first be screened to assure that they are MR safe. A powerful handheld magnet is available for such screening.
What kinds of scans or sequences are available?
NBML MR scanner has a wide range of different types of structural and functional MRI pulse sequences including 3D volume imaging, T1-weighted and T2-weighted multislice imaging, BOLD fMRI, ALS, diffusion imaging (DWI, ADC and DTI), angiography (MRA), single and multiple voxel proton spectroscopy (MRS) and single slice spectroscopic imaging (CSI).
Multi-nuclear spectroscopy (i.e., spectroscopy of nuclei other than protons) is also supported.
I need a non-standard pulse sequence implemented. Is it possible to do that at NBML?
This is not accessible yet.
Will it be possible to record ECG, pulse and respirations?
Yes. It is possible to record ECG, pulse and respirations employing PMU system.

Signal Processing

What services are provided in the signal processing laboratory?
This laboratory services are divided into two main categories, which include EEG data processing and task implementation. EEG data processing is also performed in the fields of time and frequency analysis, ERP analysis and QEEG analysis.
What is the file format of analysis results?
The results obtained from the analysis can be presented in MATLAB, Excel, and image formats according to the choice of the researcher.
What are the limitations in determining the requested output?
Signal processing laboratory services include a specific range of analysis such as frequent time & frequency domain features, and plotting scalp topographies. Some services such as classification, implementation of machine learning algorithms and extraction of connectivity features are not provided for now.
Which programs and toolboxes are used for data analysis and protocol design?
The data analysis is done in the MATLAB program using the EEGLAB and BBCI toolboxes, and the Psychtoolbox and BCI2000 toolboxes are used for task designing.
How can I get informed about the current state of the project?
At the beginning of the project, the researchers (student and professor) will receive an email from the lab expert who is responsible for their project. If there is any further questions or problems regarding the project, they can contact the relevant expert by using the provided email.
Is it possible to analyze pilot data earlier than the specified time?
The lab has made it possible for researchers to get the results of the pilot data earlier than the designated time so that they can make possible adjustments to their final protocol. It is worth noting that only pilot data analysis is done out of turn and the continuation of the project will be done according to the given time.

cognitive assessment

What is being evaluated in cognitive assessment?
A range of cognitive functions such as memory, attention, speed of information processing, ability to reason, judgment, problem solving, linguistic functions, language skills, etc., along with behavioral and emotional functions, are evaluated in cognitive assessment.
Why choose CANTAB for cognitive assessment?
CANTAB measures cognitive function, and identifies levels of performance and impairment in the brain. The technology is used in thousands of clinical trials, hospitals, and academic institutions around the world.
What are the cognitive tests included in the CANTAB test?

Attention and Psychomotor Speed
Executive Function
Emotion and Social Cognition

Which diseases are recommended for cognitive assessment by CANTAB tests?
Alzheimer's - Attention deficit disorders - Autism - Depression and affective disorders - Down's syndrome - Epilepsy - Huntington's disease - Multiple sclerosis - Obsessive compulsive disorder - Parkinson's disease – Schizophrenia - Stroke - Traumatic brain injury
What are the specifications of the CANTAB test?
CANTAB is language-independent, culturally neutral, and non-invasive and require no prior knowledge to work with computers.


What kind of data is available from IBMB?
Currently, imaging data are available including MRI, CT and X-ray. Biosignals and cognitive as well as clinical assessments will be added to the biobank shortly.
What kind of additional information is provided to the researcher?
At this phase a technical report is attached to each specimen and provided to the researcher. A clinical structured report for images and biosignals will be added to the biobank in next phases.
How the biobank can be reached?
Any researcher can create an account on the website: ibmb.nbml.ir for free and after defining a particular research project, the requested samples will be delivered to the researcher upon availability. Further information on step by step interaction with IBMB is available through the website. IBMB services are free at the moment.
How someone can contribute to IBMB and what are the benefits?
IBMB is ready to exchange MOUs with any person or institution who has research data. They will gain different kinds of benefits including free access to NBML services.
How long it will take to get the data from IBMB after the request?
After submitting a request, the samples and attached information will be available after two working days should the request fulfill the criteria and get approval by the IBMB office and NBML.
How the intellectual property of IBMB samples are handled?
All sample are published in IBMB after obtaining informed consent from the patient. Also, all research data will become available for use by written permission of the researcher who are able to set the sample availability conditional.

Image Processing

What are the image modalities that are included in image processing lab services?
There is a wide range of MRI modalities that we have routine analysis procedures for them, including Resting State and Task-Based fMRI, DWI-DTI, Relaxometry, Magnetic Resonance Spectroscopy, and Arterial Spin Labeling (ASL). For more information, please refer to the image analysis tab, services, and infrastructures part.
Is there any service available for CT, PET or other medical image analysis?
Unfortunately, not yet. We just accept MRI image processing for now.
Is it necessary to first finish data acquisition and then ask for image processing service?
It is highly recommended that you first request for a pilot analysis service. This approach will help you optimize your study design. Finally, after finishing your data acquisition, you can apply for your complete image processing service.
How long will it take to prepare image processing results from the day that the lab has received the complete data of the study?
The duration of analysis varies depending on the imaging modality and analysis approach, but it cannot be expected to receive the results less than a month after giving complete data set to image processing lab.
Is there any waiting list for the image analysis service?
It depends on the time that you apply for your service. For now, our strategy is first in first serve.
In the case of multi-modal imaging projects e.g. fMRI-DTI studies, do you charge the researcher separately for each one?
Yes, you need to pay for each analysis separately according to predefined price.
Is proper statistical analysis for each study included in the service?
Yes, depending on the study and software or toolbox, the statistical results will also be presented to the researcher.
How long it will take to analyze one subject’s data on average?
Depending on the imaging modality, it varies between 45 minutes to 2 hours.
How can researcher receive their results?
Due to large volume of image processing results they can receive their analysis results on External-Hard driver or flash memory.
Is it possible to ask for a specific part of image analysis for example can we just ask for preprocessing?
Yes, we perform analysis according to application form.

Virtual Reality

What facilities are available in the virtual reality lab?
The virtual reality lab is equipped with two setups: HTC Vive Pro and Oculus rift
What is the dimensions of the game field that is covered by the virtual reality setups?
For Oculus Rift setup, it is a rectangle with a diameter less than 5m, and for HTC Vive, it is a rectangle with 3m diameter.
How we can request the game for our research?
If the requested game is already available, it can be purchased by the Lab and the cost will be taken from the researcher later.
If the requested game is not available or we need to design a game, is there any service in the NBM for this request?
For now, we do not have any game programming service, but we can provide you with some programming companies contacts.
Is it possible to run a simultaneous EEG -VR experiment?
Is it possible to apply TMS or tES to subject in VR environment?
Yes, there are some limitations regarding experimental conditions for concurrent TMS-VR.
Is it possible to have a simultaneous recording of fNIRS in the VR lab?
Not for now
Is it possible to use VR-Glasses in MRI?
No, our devices are not MRI-Compatible.

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