CAMRI:Resources

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CAMRI



Resources for users

ILAB

Scheduling

To schedule time on the scanner, you must use the iLab web site https://bcm.corefacilities.org/service_center/show_external/3684

To have CAMRI staff member reserve the ILAB calendar for you please submit the following form to CAMRI:

To request security access for a visitor please submit the following form to CAMRI:


Cancelling a Session

After a reservation is made, users have 24 hours to modify or cancel it without charge. If reserved time is not used for any reason (including subject no-show, subject failure to meet screening criteria, experimental difficulties, or any other reason) users will be charged the full rate for the unused time, unless the user reports the cancellation at least 24 hours prior to the start of the reserved time (allowing other users a chance to use the time) in which case the user will be charged at half the normal rate. Canceled time can be paid with the usual payment methods or a user's accrued pilot time.


Email all cancellation requests to camri-staff@listserv.bcm.edu


NEW SCHEDULING AND VISITOR FORMS FOR ILAB

Please submit these forms for EACH of your non-BCM visitors at the time of reservation. Each lab is responsible for submitting this documentation AT LEAST 48 hours before the requested scan time to get security clearance for their visitors. These forms need to be submitted in ONE email to camri-staff@listserv.bcm.edu. Please include all non-BCM lab members and subjects that need access. Please be aware that the pre-COVID cancellation policy is back in effect as stated below. All requests under 24 hours will automatically be denied.

Visitor Policy for Security Clearance

To request security access for a visitor please submit the following form to CAMRI:


Security requires a minimum of 24-hour notice for ALL visitors.

If bringing subjects in after hours please use the Cullen entrance to check yourself and your participants in.

For BCM Users

  1. Navigate to the core page: https://bcm.corefacilities.org/service_center/show_external/3684
  2. In the upper-right-hand corner of the screen click the green ‘Login’ button. Click BCM user, this will take you to the BCM page where you enter your BCM/ECA log in credentials
  3. Explore the website. For instance, click “Reserve Equipment” to schedule scanner time.

Adding users: You may want others in your lab to be able to book scanner time. This is a two-step process. First, the lab member will sign up for an iLab account and request to join your iLab group. Second, you will approve the request in iLab.

Step 1: Lab member signs up for account

  1. Navigate to the core page: https://bcm.corefacilities.org/service_center/show_external/3684
  2. In the upper-right-hand corner of the screen click the green ‘Login’ button
  3. Under BCM user click ‘here’ to be redirected to the authentication page
  4. Once you have entered your credentials, click the ‘Log in’ button
  5. You will be directed to an iLab Registration page where you will need to select your PI/Lab, and verify your contact information
  6. Once your registration has been submitted, your PI will receive a notification that you have requested membership to their lab in iLab. They will need to approve your membership and assign any Fund Number(s) for your use.

Step 2: Approve lab member in iLab

  1. Click here to log-in: https://bcm.corefacilities.org/service_center/show_external/3684
  2. In the upper-right-hand corner of the screen click the green ‘Login’ button
  3. Under BCM user click ‘here’ to be redirected to the authentication page
  4. Enter your BCM ID and password, and sign in.
  5. Once logged in, look for the link in the left hand menu that says 'my labs'. Hover-over and select your lab.
  6. Set the auto-approval amount if you do not wish to approve service requests below a certain dollar amount. To do this, select the 'Members' panel and enter a dollar amount in the 'Auto Pre-Approval' amount and click 'save settings.’
  7. To approve lab membership requests, select the ‘Membership Requests & BCM Fund Numbers’ tab. New membership requests will show at the top of this page. Click “Approve” to accept a member into your lab. Click “Reject” if they are not a member of your lab.
  8. To assign a Fund Number to a member of your lab, find the member in the above list where it says, ‘Manage Fund Number.’ Select the checkbox(es) to the right of their name for the Fund Number(s) you wish to assign them.


To Create an Equipment Reservation: Once you have been accepted into a PI’s lab and assigned a Fund Number, you can schedule equipment time.

  1. Navigate to the core page: https://bcm.corefacilities.org/service_center/show_external/3684
  2. In the upper-right-hand corner of the screen click the green ‘Login’ button and enter your iLab username and password
  3. Select the Schedule Equipment tab and click on the ‘View Schedule’ button next to the instrument of interest. Click and drag on the time frame you would like to schedule your reservation for.
  4. A window will pop up that will allow you to verify your reservations details and provide payment information before saving the reservation.

For non-BCM Users

Please create an account and ask everyone in your lab to sign up too.

To register for an account:

  1. Complete the registration form on the sign-up page. https://bcm.corefacilities.org/service_center/show_external/3684
  2. Receive a Welcome Email from iLab (typically within one business day) with login credentials.

Creating an Equipment Reservation. Using your iLab login credentials, you can place orders and schedule equipment time.

  1. Login using the ‘Not a BCM user?’ option.
  2. Enter the credentials received in your welcome email from iLab.
  3. Select the Schedule Equipment tab and click on the View Schedule button next to the instrument of interest. Click and drag on the time frame you would like to schedule your reservation for.
  4. A window will pop up that will allow you to verify your reservations details and provide payment information before saving the reservation.

Problems

At BCM, the contact people for iLab are Jay Villarreal and Myeshia Brown. They can be contacted at ilabs-support@bcm.edu At iLab, login to iLab and click on the “leave iLab feedback” link in the upper right hand corner or contact support@ilabsolutions.com

Here are iLab links for online user guides http://help.ilabsolutions.com/core-facilities-customers http://help.ilabsolutions.com/core-facilities-lab-administrators

Flywheel

Click here for the CAMRI Flywheel server (NB: this only works inside the BCM firewall; if outside, you must VPN in)

All data is the user's responsibility. Data on the scanners is not stored or archived and may be deleted at any time. Users should back up data to CDs or push to the Flywheel server after every scanning session to avoid loss of data. Users are also urged to view their data as soon as possible after scanning so that any problems or errors can be diagnosed before the next subject is scanned." CAMRI is not responsible for lost data and we do not transfer or back up data from scanners. Transferring back up data to this resource is the responsibility of the users.

Uploading Data to the database

To have your Session Imported into the flywheel database please follow these instructions.

• Start your Subject Registration by opening the Patient Registration Screen and start entering registration fields as usual.

• To Opt-in and have your session automatically imported into the database enter flywheel in the Accession Number Field.

• You will also need to enter a Subject ID, Group ID and Project Name in the Additional Info Field using the format shown below.

                              subject_id@Group_id/project_name

• Please see your PI or CAMRI support staff if you do not have your Subject ID, Group ID or Project Name.

Siemens Patient Registration screen

Note: If you mistype your Group and/or Project name, your data will likely still be sent to Flywheel. Please contact the CAMRI support staff so that they may assist in updating your database session info.

• If you do not enter these values at the beginning of the scan, you can do it later by going to the Patient Browser, selecting the exam, selecting Edit/Correct and entering the required values specified above.

Accessing data you have already uploaded to the database

To View and download your Sessions please follow these instructions.

Click here to log in to Flywheel (NB: this only works inside the BCM firewall; if outside, you must VPN in)

• Please Click on the G+ Sign in to sign in with the Google plus credentials your PI or CAMRI support staff has provided for your group.

Gplus.png

• You will see a listing of your groups sessions in the database.

Flywheels1.png

• To download the session to your desktop please select one or more of your sessions.

Flywheels2.png

• Click on Actions and Select Download. Select a location to save this session on your Desktop.

Flywheels3.png

Complete Flywheel documentation is at docs.flywheel.io

NOTES

CAMRI Policy on Unexpected Events

If an unexpected, unusual or untoward event occurs during a scan, please send an e-mail with a brief description of the event to camri@bcm.edu as soon as possible. This will allow CAMRI to be responsive and proactive in addressing any issues. The e-mail does not need to be lengthy but is required for both scanner-related and subject-related events. Example e-mails:

  1. “We were scanning today at 2 p.m., and the patient complained of back pain after 45 minutes, so we had to end the scan early”
  2. “In the middle of our third functional scan, the scanner crashed and had to be rebooted”
  3. “the BOLDscreen was flickering during our functional runs”

In addition to specific problems that you encounter, we always welcome user feedback on CAMRI operations.

Adverse Event Reporting to IRB

The CAMRI requirement to report unexpected events is distinct from the enduring requirement to notify the IRB of any adverse event occurring to human subjects enrolled in a protocol. An adverse event is defined as “any untoward medical occurrence in a participant, which does not necessarily have a causal relationship with the trial intervention. An adverse event (AE) can, therefore, be any unfavorable and unintended sign (including an abnormal laboratory finding), symptom, or disease.” For more information, please review the highlighted section (pages 150 - 151) in the BCM IRB Manual. Media:irb-manual.pdf

Saving Data

There are three ways to save the data that you have collected at great expense. CAMRI does not back up data. Users are responsible for saving their own data!

Method 1 (Easiest): Use the Flywheel Server

Please click on the Flywheel tab above or go to https://openwetware.org/wiki/CAMRI:Flywheel for further instructions on backing up data using that resource.

Method 2: Use Box

This requires that your lab have a Box account; contact Dave Lee (dlee@bcm.edu) to obtain one.

  1. Select "Transfer" on the Console
  2. Click on the folder that you would like to transfer to Box.
  3. Once folder is highlighted click on the 'Transfer' tab in patient browser window and click Export to Offline.
  4. This will open a window. Click "\\mrisrv\scans" under path
  5. Add a Forward slash (\) and type your PI name (e.g. "Beauchamp") and another (\) and type name of folder you are sending. Ex: \\mrisrv\scans\CAMRI\Phantom
  6. Hit 'OK' and another window will pop up telling you that this path does not exist and would you like to create it, click yes.

Media:Sendingtobox.docx


To Access the data: Go to the Box website and go in to the directory "PI Name".

Method 3: Burning a Backup Disk

  1. Once you are done scanning and you want to make a back up disk. You need to open the patient browser. You can do this by clicking Patient -> Browser.OR- Click the browser shortcut button on the bottom right of your keyboard. (Three folders icon)
  2. This will open the patient browser screen.
  3. Before you select the scan you would like to burn you will need to insert disk into disk drive for burning. To do this click: Transfer->EJECT FROM DVD-R.
  4. Once the drive opens, insert Blank disk and close it. You will see a message at the bottom of your screen saying that disk in DVD R is locked for burning. Once you see this you are able to burn to it.
  5. Locate under the Local Database the name of the scan you just did. (It is organized by date so it should be last scan done)
  6. You can select the entire folder to burn or you can use CTRL and click the individual scans you would like to burn to disk.
  7. Once you have the folder or individual scans that you would like to burn highlighted click: TRANSFER-> EXPORT TO. Then a dialogue box will pop up with DVD-R highlighted just click EXPORT.
  8. Once you hit export another box will pop up where you will be able to name it. Click Viewing tool if you or your patient will be viewing it on computer. (MOST PEOPLE CLICK VIEWING TOOL)
  9. The status of your disk will be shown on the bottom part of screen, it will show a red circle when recording. Once it says Recording was successful at bottom you can click: TRANSFER-> EJECT FROM DVD-R.
  10. Then take your disk and close the disk drive.


Human Subjects Protection

To scan at CAMRI, approval from your home institution institutional review board (IRB) or committee for the protection of human subjects (CPHS) is required. Click here for an IRB proposal template.

MRI Data Analysis

Click here for more information on MRI data analysis.

Change Log

Notes on Recent Changes to Our Equipment.

Updated scanner 5 to new computer and imager. Still running at VB17 software.

Scheduling and Visitor policy

To schedule or cancel time on the scanner, you must use the iLab web site https://bcm.corefacilities.org/service_center/show_external/3684 Click here for detailed instructions.


When scheduling your participants please send their full name and who from the lab will be escorting them on campus to ljberry@bcm.edu and krunge@bcm.edu to ensure security clearance. Security requires a minimum of 24-hour notice for ALL visitors.

If bringing subjects in after hours please use the Cullen entrance to check yourself and your participants in.

About CAMRI's Siemens Scanners

The BCM CAMRI has 2 whole-body 3T Siemens Scanners labeled 3T-4 and 3T-5.

Scanner 3T-5 is a Magnetom PRISMA Fit (newly upgraded July 2021) with a Head/Neck 20 channel, Head/Neck 32 channel, Head/Neck 64 channel, Spine 32 channel, Flex 4 Large, Flex 4 Small, and body coil.

Scanner 3T-4 is a Magnetom PRISMA Fit with a Head/Neck 20 channel, Head/Neck 64 channel, Spine 32 channel, Flex 4 Large, Flex 4 Small, and body coil.

More information about the difference between the coils can be found here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538896/

Both scanners have a bore inner tunnel diameter of 60 cm.

Troubleshooting

Report all issues to camri@bcm.edu

http://openwetware.org/images/0/01/CAMRI_MRI_Safety_Manual.pdf

There are a few helpful videos that you can watch on YOUTUBE that will help you become a little more familiarized with our systems here at CAMRI. Here are the links: https://www.youtube.com/watch?v=pi1OLUflhTU


Having problems with...

  1. PC or MAC computer? Call Dave Lee at 713.798.5517 during normal business hours (M-F 8a-4p)
  2. Response devices? Go to "how to scan" tab. Click on "response recording". Open the document created by Jung Hwan for fORP confirgurations.
  3. Button boxes? Go to "how to scan" tab. Click on "Button Boxes"
  4. MR Scanners? a) Is the error message for a software issue? Restart the scanner. Start by going to SYSTEMS tab at the top of the screen. Click END SESSION. A blue box will appear. Select RESTART SYSTEM. Wait for system to restart. This could take 5-10 minutes. b) Is the error message for a hardware issue? Shutdown the scanner. Start by going to SYSTEMS tab at the top of the screen. Click END SESSION. A blue box will appear. Select SHUTDOWN SYSTEM. Wait for system to shutdown completely. The screen will go black and tell you it is okay to turn off the system. Go the switch on the wall and push the blue button that says SYSTEM OFF. Wait about 10 seconds and push blue button that says SYSTEM ON. The system will come back up. This could take 10-15 minutes. Is the scanner working properly now? If no, call Siemens Service at 1.800.888.7436 and give them functional location number listed on the phone list by the quench button. Also log error message in the log book next to the keyboard.
  5. Visual Simulus? a) Projector? Make sure the switch is turned to PROJECTOR. Turn projector on with remote located in cabinets. If problems persists, please call Dave Lee at 713.798.5517. b) BOLDScreen? Make sure the BOLDScreen is turned on in the scan room. Make sure the switch is turned to BOLDSCREEN. If problem persists, go to "how to scan" tab. Click on "visual stimulus display". Open the link to the Cambridge Research Systems BOLD Screen User Guide for troubleshooting problems.


Stimulus computer and button boxes check list: There are several ways to configure the interface box. Here is a sequence that you can use to make sure it is set up properly:

  1. Connect your desired button box in the magnet room
  2. Push the main rotary knob on the interface box and follow prompts to set it to the desired mode. You must do this every time you scan.
  3. Push the correct button on the switch box to route the outputs of the interface box to your chosen computer.
  4. Start your stimulus software on the computer.

The sequence of operation is important so make sure it is done in this order.

Response Recording

Responses are recorded with a fORP system. Link to Jung Hwan's user guide here: fORP Configuration



Bold Screen Setup

For Scanner 5 Bold Screen Setup: Media:Scanner5.docx

For Scanner 3 Bold Screen Setup: Media:Scanner3.docx


Console Cam

The Console Cam is provided for users to obtain scanner console support remotely from CAMRI staff without the staff member having to enter the room. It will broadcast an image of the console and allow voice communications via Zoom conferencing.

Please use the iMac in the control room that is next to the Scanner Console to use the Console Cam. You can use this account to log into the iMac;

    account:  camri
    password:  camri  

After you are logged in start a new meeting in Zoom and copy the invite to the clipboard.

You can then use your own web mail to paste the invite info and send the email to the person you are requesting support from.

The arm of the Console Cam is flexible and you may have to adjust it so that the screen is centered so that the viewer can see the entire screen.

Visual Stimulus Displays

3T-3 and 3T-5 display visual stimuli on direct view LCD screens.


3T-5 uses a Cambridge Research Systems [32" display with resolution of 1920x1080]. This display requires a video adapter with a DVI-D (dual link) connector. There are currently adapters for Macs connected to the display switcher.

3T-3 uses a [24" display with resolution of 1920x1200]

Link to manual here: Cambridge Research Systems BOLD Screen User Guide The BOLDScreen has a built-in color profile that can make images appear too dark. Instead, use the default color profile as follows:

  1. On the Mac laptop stimulus computer, Click on the Apple, Open "System Preferences"
  2. click on "Displays", select the "Color" Tab
  3. Select the "Color LCD" profile for the second display (the BOLDscreen)

Ricky Savjani has redone the gamma calibration on the 3T-5 BOLDscreen, this can be accessed in PsychToolbox as follows. First, Click here to load the table

 % load in the gamma table
 load CRS_32BOLDSCREEN/gammaTable_Spline_fit.mat
 % after opening a window, call this to load the load the gamma table to to your Screen
 Screen('LoadNormalizedGammaTable', win, gammaTable2*[1 1 1]);

Now, desired intensity levels will be mapped appropriately to the screen.

Rough calculation of image size in degrees of visual angle: roughly 76.5 cm from screen to eyeball height of screen is 13.7 in = 34. 8 cm width of screen is 34.8 * (1024/768) = 46.4 cm atan(23.2/76.5) = 0.29 rad = 16.6 degrees ~30 degrees full width

Audio (headphones)

Oneway to deliver auditory stimuli to your participants is through the headphones. These are Siemens equipment and are controlled by the scanner. First, make sure the headphone cord is plugged into to your stimulus presentation computer (laptop, desktop, boombox, etc). Then, plug the other end into the back of the intercom box (the same one that's used to speak with the participant while they're in the scanner.)

If you're not hearing anything, go to Options -> Configuration. A new window will pop up with icons. Choose "Patient Comfort." In the next window, make sure the volume bars under "Music" are not at the very bottom (which is the default.) . The speaker icon indicates sounds send to the room, and the headphone bar is specific to sound sent through the headphones.

AudioConfiguration.png

ASL Help

This ppt describes the units when you draw an ROI on the relCBV map (BW). You cannot draw on the Perfusion Color map the units are not scaled.

Media:ASL.ppt

Quality Assurance

Weekly QA scans are performed on both the Prisma and Trio scanners. Below are the results of the previous 52 week EPI QA runs.


PRISMA 52 Week EPI QA

QAS4.jpg


TRIO 52 Week EPI QA

QAS5.jpg

Sequences to Use

What pulse sequence to use for fMRI

There are a variety of different pulse sequences that can be used for fMRI, including the standard Siemens EPI product sequences; multi-band EPI sequences from MGH and Univ. of Minnesota; and spiral sequences implemented by David Ress.

Siemens EPI product sequence with GRAPPA 3, TR = 2 seconds


MGH Blipped CAIPI multi-band EPI with SMS 2, GRAPPA 2, TR = 1.5 seconds Images show activation maps overlaid on tSNR maps (NOT raw EPI images). The task was one run listening to an audiovisual story. mean tSNR is higher with MGH, 171 vs 148 maps. There was more activation with MGH, likely as a result of more statistical power with 160 (TR=1.5) vs. 120 (TR=2) time points. 16432 voxels were activated with the task vs. 15349 voxels (positive activation only, q = 10-7 for both)

Here is another analysis of the same data by David Ress. The results are similar, with the G2, MB2 version winning by around 15% in fSNR over the product sequence. But, the shorter TR will also net you an improvement of ~5% in CNR in a similar length run. It is also interesting, however, that the G3 run had less aliasing artifact, suggesting that shorter acquisition times reconstruct more cleanly.

Siemens EPI product sequence with GRAPPA 3, TR = 2 seconds

MGH Blipped CAIPI multi-band EPI with SMS 2, GRAPPA 2, TR = 1.5 seconds


MGH Blipped CAIPI multi-band EPI with SMS 2, GRAPPA 3, TR = 1.5 seconds

Similar results were obtained with a phantom:


Siemens EPI product sequence with GRAPPA 3, TR = 2 seconds

MGH Blipped CAIPI multi-band EPI with SMS 2, GRAPPA 2, TR = 1.5 seconds


MGH Blipped CAIPI multi-band EPI with SMS 2, GRAPPA 3, TR = 1.5 seconds

What T1-weighted Anatomicals to Use

Most studies collect at least one scan with structural contrast in order to align their other runs (functional, DTI, etc) to other participants and to published atlases. In some cases, measurements such as volume or cortical thickness are also derived from these scans. We have tested a few of these on the Prisma (Bay 4) and will run similar analyses on the Trio (Bay 5) soon. CAMRI (specifically, Meghan) recommends the following scans for new studies, and can easily set these up in your protocol:

(1) 1mm isotropic scan. Acquisition time: 4:01. Contrast to noise ratio (CNR): ~2.0. This is a good choice if speed is of the essence, and your main goals are alignment of lower-resolution scans.

(2) 1mm isotropic scan. Acquisition time 5:12. CNR: ~2.6. High quality T1 scan that will suit most studies. Very good CNR.

(3) 800um isotropic scan. Acquisition time: 6:38. CNR: ~2.2. A happy medium between speed and resolution.

(4) 700um isotropic scan. Acquisition time: 8:18. CNR ~ 2.2. Based on the HCP sequences. This is recommended if your study would benefit from higher resolution. For instance, if you plan to do cortical thickness studies or are interested in segmentation of fine structures, this could be a good choice.

A note on CNR: This was calculated from only a handful of people (sometimes, just from one participant). CNR was calculated using FreeSurfer segmentations of the cortical ribbon and the white matter mask. CNR=(Mean(white) - mean(grey)) / mean(std(grey), std(white)). Signal was taken from the raw image, with prescan normalize turned ON.

Misc Notes

Slice Ordering

David Ress' former student Andrew Florens examined the acquisition time stamps and found that axial slices are collected from Superior to Inferior (head to foot). If an odd number of slices is acquired, the slice order is

 1, 3, 5, 7, etc.
 2, 4, 6, 8 etc.

If an even number of slices is acquired, the slice order is reversed:

 2, 4, 6, 8, etc.
 1, 3, 5, 7, etc.

Editing Dicom Headers

Information regarding how to edit and anonymize DICOM images can be found:

Media:How_to_anonymize_and_edit_Dicom_headers_utilizing_Sante_Dicom_Editor.pdf