Scanner operation

• What can I do in Research Mode?
• How can I enable Research Mode?
• I want to use spep pulse sequence for spiral acquisitions. How should I set it up?
• I need raw data files (P-files) produced by regular GE ("product") sequences. How can I get them?
• When copying slice prescriptions from previous scan using Copy RX button in the Graphic RX screen, should I use Present Loc or Original Loc? They seem to be doing the same thing.
• How do I delete protocols?
• How do I know if a protocol needs to be updated?
• Should I use top-down or bottom-up phase encoding view order for fMRI?

•  What can I do in Research Mode?

Research Mode enables the following functionality:
-Non-product (e.g. home-grown) pulse sequences can be run safely in this mode. Popular spep (for spiral 2D acquisition and ASL imaging), and 2dflash for field-map acquisition require this mode in order to run.
-For functional imaging protocols timing parameters, such as TR and # reps (and also blocking of on-off conditions) can be entered directly via fMRI screen.
-When running functional scans, BrainWave RT (real time) GUI can be bypassed.

•   How can I enable Research Mode?

Occasionally (e.g. after system reboot) the scanner may be left in the clinical mode. In that case, in the Rx Manager window click the button Scan Modes, and select Research Mode.

• I want to use spep pulse sequence for spiral acquisitions. How should I set it up?

A PDF file with instructions for using the spep pulse sequence for non-ASL imaging can be found here.

•   I need raw data files (P-files) produced by regular GE ("product") sequences. How can I get them?

Make sure research mode is enabled. Save series by pressing Save Series button, and press Prepare to Scan button. Go to CV page by right-clicking mouse on the big button Research Options in the lower left corner of the screen(it shows up only after pressing Prepare to Scan button) and select Display CVs. In the CV name field type in autolock and set its value to 1. Close the CV window.

• When copying slice prescriptions from previous scan using "Copy RX "button in the Graphic RX screen, should I use "Present Loc" or "Original Loc"? They seem to be doing the same thing.

Original Loc should be used to copy the prescription from previous functional (fieldmap) scans to the current fieldmap (functional scan) prescription.

• How do I delete protocols?

1. Whenver there is an major upgrade of the MRI system.
   
2. Go to protocol manager (the top-middle icon of the 6 icon cluster on the top left corner of the screen)
3. Click “protocol Rx” button
4. Find your protocol by choosing a category (e.g., Head, Neck/Cervical, ...)
5. Double check the protocol name and make sure it is the one you want to delete (Do NOT delete protocols that don't belong to you)
6. Right click on the protocol name and select “cut”
7. Confirm
8. Repeat steps 3-6 to delete more protocols

If you have questions on how to safely remove protocols, please contact Kun Lu ( kunlu@ucsd.edu )

• How do I know if a protocol needs to be updated?

1. Whenever there is major upgrade of the MRI system.
   
2. If you have not used the protocol for more than 6 months, it probably needs to be updated.
3. The protocol does not run / gives error messages.
   
4. If you are using FSPGR for T1-weighted structural scans on 3teast, you need to update it to BBFSPGR.
5. If you are using BBFSPGR for T1-weighted structural scans on 3twest, you need to update it to FSPGR.
6. If you are using BrainWave when running EPI scans, you need to switch to research mode.
7. Pay close attention to the center updates distributed through the E-update and the Cfmri website. Update the protocol as necessary when we announce new pulse sequences and new methods.

Please direct questions to Giedrius Buracas ( kunlu@ucsd.edu)

• Should I use top-down or bottom-up phase encoding view order for fMRI?

The Center recommends bottom-up view order for fMRI. Using top-down view order may generate more gradient heating. However, one may choose to use top-down view order for the following considerations:

1. The geometric distortion has less impact to the region of the interest in top-down than in bottom up view order.
2. more slices or better spatial coverage is needed while no other means can achieve that.

Please continue reading for details about the above mentioned considerations.

Phase encoding view order refers to the direction in which the Kspace is acquired. In top-down view order, acquisition starts from the top the Kspace; whereas in bottom up view order, acquisition starts from the bottom of the Kspace. Please note that phase encoding view order is not the same as phase encoding direction. Phase encoding direction refers to the physical dimension in which the phase encoding gradients are applied, e.g. left-right, anterior to posterior, or superior to inferior. Each phase encoding direction can have either bottom up or top down view order.

Because Kspace is acquired in opposite directions in top-down and bottom-up, the off resonance effects in MRI images (e.g. geometric distortion, chemical shift) are opposite. A good example on the GE 3T scanners is: when acquiring axial EPI images in human with anterior-posterior phase encoding direction, bottom-up view order causes the voxels to shift towards the anterior, whereas the top-down view order shifts the voxels towards the posterior. The voxel shift causes either stretching or compressing of the targeted brain region. In general, stretching is preferred over compressing as stretching is easier to correct using field map correction algorithm.

Additionally, in GE's implementation of top-down view order, partial K space is always used (only the top half of K space is acquired). Whereas in bottom-up view order, full K space is used by default. Therefore more slices can be acquired in a same TR with top-down than with bottom up, providing bigger spatial coverage. The caveat of using top-down view order at the maximum slice/sec rate is that the gradient heating becomes more severe.