MR Protocols: Difference between revisions

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== '''Gradwarp''' ==
This page offers advice about how to set up your scan protocols and save the information.  The wiki pages take you through the template protocols we think are most widely used. These protocols can be found on the the scanner console, saved under “CNI/head” within the protocol pool.


* By default, the scanner applies a correction for nonlinearities in the gradients, called gradwarp.  Presumably, the correction will make your images more spatially accurate.  It is not clear exactly what is the nature of the correction.
Screenshots to remind you about how to set specific MRI protocols can be found on the page [[Setting up protocols page | Setting up protocols]]
* Currently, Atsushi's spiral sequence does not take the gradwarp into account; thus, spiral images may be (slightly) misregistered with respect to images from stock GE sequences.


== '''"Silent" Partial Fourier''' ==
= General =


* In EPI, if you increase the acquisition time too much (e.g. by having a large matrix size or a short TE), the pulse sequence will be unable to acquire the requisite half of k-space before the TE value. When this happens, the scanner silently decides to simply drop that half of k-space and acquire a default of 8 lines of k-space for that half.  This is potentially quite bad, as you lose a lot of SNR.  Moreover, there will be wasted dead time after the RF pulse up until the beginning of the 8 lines. The safest way to see whether the silent dropping of k-space happens is to check the plotter (to do that, start scanning, pause the scan, and then run plotter from a command window).  An easier (but unverified) way is to monitor the Relative SNR number in the console.  It appears that once you go over the limit, the relative SNR jumps way down.
== Setting up an MR scan protocol ==
** There is weird buggy behavior in the console concerning the relative SNR number.  If you violate the limit and the number of slices that can be acquired is less than the current number of slices (resulting in # acqs being set to 2), you need to reset the number of slices to a lower number within the limit.  Then, the # acqs will go back to 1, as desired.
A basic MR scan session usually starts with the following scans:
** Regarding using the relative SNR as a index for whether the silent partial fourier occurs, for some reason, you need at least 20 volumes prescribed.  I have found that if you prescribe less volumes, then the big jump in relative SNR does not occur.
* '''Localizer''' - a 3-plane localizer or 'scout' scan meant to find the subject's head. It is also be used for prescription for the subsequent scans. Doing some sort of localizer is necessary, and the '3planeloc SSFSE' (single shot fast spin echo) is the standard work-horse used by most CNI users.
* To deal with the "silent" partial Fourier issue, one strategy is to ensure that you always get full coverage of k-space.  This may be preferable simply due to the reason that partial Fourier strategies may result in data that have problems in the reconstruction process.
* A different strategy is to ensure that you get the maximal number of lines of k-space (not the default 8 lines). It is not clear how to do this (perhaps CV variable num_overscan?)


== '''Fermi filtering''' ==
* '''Anatomical''' - usually a 3D T1-weighted scan at 0.9mm or 1mm isotropic resolution. It is essential for image alignment and anatomical analysis. More choices of anatomical scans are listed in the Anatomical imaging section.


* The reconstruction code applies a Fermi low-pass filter by default(!). To turn this off, set CV var rhfermr to the matrix size and set CV var rhfermw to 1.
* '''ASSET calibration''' - a calibration scan for parallel imaging. It should be run before any scans that will use ASSET, such as GE's conventional fMRI and diffusion scans.  


== '''Reconstructed image size''' ==
* '''Higher-order shim''' - measures the magnetic field inhomogeneity and corrects it with polynomial gradients up to 2nd order. It should be run after ASSET and before fieldmap, fMRI or diffusion scans.


* By default, images are reconstructed at matrix sizes that are powers of two (presumably for speed).  However, this wastes disk and memory space.  To change the reconstructed image size, set CV variables rhrcxres,rhrcyres,rhimsize.  For example, if I acquire a 70 x 70 matrix size, I would set rhrcxres=70, rhrcyres=70, rhimsize=70, and then I would get 70x70 images instead of 128x128.
* '''Field map''' - measures the magnetic field inhomogeneity that cannot be corrected by the shim and saves the inhomogeneity in a field map. It should be run immediately before or after the fMRI scan.
* But be careful --- it appears that one you set these CV vars, they will no longer default to the next highest power of two if you change parameters of the sequence.  For example, in one instance, I was increasing the matrix size but forgot to change the CV vars, and the resulting reconstructed images were totally corrupted.


== '''Precise values''' ==
At this point you will want to add a number of '''functional''' scans, '''diffusion''' scans or other type of scans based on your experiment. In the [[#MRI Protocol Templates | next section]] we describe templates for different categories of MRI protocols. The protocol templates are organized by category.  One set is based on conventional multislice (2D) or 3D methods, a second set is based on the new simultaneous multislice (SMS) protocols (also called mux or multiband), and a third set are some special methods (spectroscopy and qMRI).


* The GUI tends to round values that you enter.  For example, if you enter 1605.242 for the TR, the GUI will round the value displayed to 1605.2, but the value that actually will get used is the precise one.  You can check this via the CV vars (e.g. optr), which you can take to be the actual value used.
You can get help in customizing the parameters from the CNI staff (ask Hua, Adam, or Laima).
* If you enter in a precise value, and copy and paste the entire sequence, usually I find that the precise value is also copied.
* If you enter in a precise value, and then save the protocol, I have found that (at least in some cases) the wrong, rounded value is saved.  You should re-enter the precise value every time you load in the saved protocol.
* If you have a precise FOV size (e.g. 14.24 cm FOV) entered, and you copy that slice prescription to another sequence, I have found that the rounded FOV is copied (e.g. 14.2 cm FOV).  You should re-enter the value to get it right.


== '''CV variables''' ==
== Saving your protocol parameters ==
=== Save screen-shots ===
At the GE console, you can save screen shots of the GE interface to show the main parameters that you have set in a protocol. Just get to the screen that you want to save, then press the 'Prnt Scrn' button on the keyboard. A little dialog will show up. You can choose to print, which will print on paper to the Laser printer in the control room. However, we strongly suggest that you save some trees and the toxic ink chemicals by saving a digital copy instead. To do this, type ina reasonable name in the filename field (default is 'screen') and hit the 'PNG" button. A PNG image will then magically appear in the 'screensaves' folder on the linux machine next to the console (cnirt). From there, you can email the images to yourself. Or, even better, create your own personal wiki page here that describes your protocol (just log in with your SUNet ID) and put the images in there. Then, you will always have them available when needed! THis is also a great way to share protocol information with your colleagues.
=== Get a PDF of all protocol parameters ===


Many variables that control scanner behavior are not accessible via the usual GUI interface. To access these variables, press Save Rx and then Research->Download. Then, select Display CVs.
You can get a complete PDF of all your protocol info with a few clicks of the mouse. It's not quite as easy as a screensave, so we outline the procedure here. Note - There is a change on figure 4 - The pdf file will now appear with some viewing options at the top of the pdf file. By clicking on the 4th option from the right (a square with three parallel lines) the drop down menu will display a "save a copy" option which will result in the pdf being saved in the screensaves folder on the Linux machine (voxel2) next to the scanner.


Here is a list of CV vars that Kendrick has run across.  Atsushi might know about more of them.
<gallery perrow=5>
Image:Export_protocol_button.png|Click the "Protocol Exchange" button under the Image Management tab.
Image:ExportMode.png|Select "Export Mode" and click OK in the dialog that comes up.
Image:ProtocolSelection.png|Find your protocol in the next dialog, drag it to the "Protocol Selection" panel, and make sure it is selected. Then press the "preview" button.
Image:SavePdf.png|You'll then see the PDF of your protocol. Right-click anywhere within the pdf and select "Save as..." from the drop-down menu.
Image:SaveAs.png|Type the path and filename. Be sure that the path is /usr/g/mrraw/screensaves/ so it'll magically appear in the "screensaves" directory on the linux box.
</gallery>


  '''YOU MAY VERY WELL WANT TO USE THESE:'''
== MRI protocol templates ==
  map_deltaf [frequency for echo time difference (for Atsushi's spiral fieldmap)]
The CNI has stored example protocols for anatomical, fMRI, diffusion, spectroscopy and quantitative MR scans (named as "CNI Examples", stored under "CNI / Head"). Depending on the user's needs, there are several ways to run a scan session. The stored protocols are meant to be used as a 'menu' from which you select the sequence that you want, based on your needs. While there are many variations stored there, here we just highlight a couple of the most common versions. A detailed list of all parameters for all scans can be found in the PDF files for each protocol. Some suggested ways of selecting from and set up these scans for your own scan session are described below.
  rhfermr [Fermi radius (in matrix units I think)]
  rhfermw [Fermi width (in matrix units I think)]
  rhrcxres [transform size (x)]
  rhrcyres [transform size (y)]
  rhimsize [image size]
  pepolar [phase encoding polarity (direction)]


  '''YOU PROBABLY DON'T WANT TO USE THESE:'''
== Moving protocols from CNI to Lucas ==
  opslquant [number of slices]
If you plan to transfer scan protocols from the CNI to Lucas Center, please contact Hua and follow the steps below:
  optr [TR]
  opfphases [number of TRs]
  opte [TE]
  opflip [flip angle]
  opfov [field-of-view]
  opxres [frequency-encode resolution]
  opyres [phase-encode resolution]
  opslthick [slice thickness]
  opphasefov [fraction of the FOV in the phase-encode direction]
  avminte [minimum TE, same as in GUI]
  opnex [number of excitations]
  nograd [no gradwarp, default is 0]
  rhferme [Fermi eccentricity??]


  '''UNKNOWN/UNTESTED:'''
* Let CNI staff know the (a) name of the protocol(s) to transfer and (b) which Lucas scanner. It would be useful if you could include a list of scans in your protocol too. We will help transfer the protocol files over to Lucas.
  nframes [number of frames?]
  opti [?]
  num_overscan [default is 0?]
  rhmethod [default is 1?]
  esp [echo spacing?]
  autolock [autolock raw files, default is 0]
  rhrcctrl [controls what data are saved; 4-bit mask: imaginary, real, phase, magnitude; 3 means phase+magnitude]
  rhexecctrl [?]


== '''Fieldmaps''' ==
* If your protocol contains pulse sequences provided by researchers outside CNI, then please let them know about the transfer so that they can prepare the sequences for you at Lucas. For example, if you run any spectroscopy sequences, then please let [mailto:mgu@stanford.edu Dr Meng Gu] know about the transfer plan.


One of the major problems that affects EPI data is spatial distortion. It is possible to correct for distortions in EPI data posthoc using fieldmap measurements. Kendrick has developed some MATLAB code that handles spatial distortion and other pre-processing procedures relevant to EPI fMRI data.
* Follow up with Lucas staff about setting up peripheral devices, e.g. response box, scanner trigger, visual display, physio recording, etc. The visual display at both Lucas scanners uses a projector and a screen mounted on the head coil. Another thing to keep in mind is that '''Lucas scanners do not send out scan triggers in the same way as the CNI scanner does''', so it’s preferred to let the stimulation program trigger the scanner by writing out a byte through the usb-serial port. Lucas also provides their version of the functional sequences that send out triggers to the computer, if you prefer to let the scanner trigger your stimulation. For more details please seek advice from the Lucas staff.  


The process can be divided into two basic parts. The first part is getting the fieldmap acquisition right. The second part is using the code to process the EPI and fieldmap data.
* The Lucas center has its own instance of Flywheel [http://lucascenter.flywheel.io lucascenter.flywheel.io]. '''Prior to scanning at Lucas, please be sure to coordinate with Tom Brosnan, or [mailto:lmperry@stanford.edu Michael Perry], to have your group’s accounts and projects configured.''' Michael can help you make sure your projects have the correct gear rules configured to process your data, which is an important consideration to maintain consistency across the two sites. As a good first approximation you can map existing project gear rules at CNI to your new projects at Lucas. Our goal is to make the same gears available at Lucas as are available at CNI. This is a work in progress.


Note that the information presented in this section is not yet complete (e.g. one big missing part is how to actually run the MATLAB code, and another missing part is the conceptual background of all this fieldmap stuff).
= Conventional imaging =


'''Fieldmap strategy'''
== Anatomical imaging ==


The higher-order shim (HOShim) is quite important and massages the field to be as homogenous as possible. (It's best to get the field right up front instead of relying on postprocessing!).  In the HOShim, you should probably prescribe an ellipse that is liberal, i.e. covers all parts of the brain that are within your slice prescription.  Covering some air outside the brain is fine.  After the HOShim, make sure the Shim setting is OFF on all subsequent scans.
===T1 weighted ===
All the suggested T1-weighted scans use GE's "BRAVO" sequence. It is an IR-prep, fast SPGR sequence with parameters tuned to optimize brain tissue contrast. Unless you have good reason to do so, you probably don't want to play with any parameters other than slice orientation, voxel size, and bandwidth. And for those, most users just pick one of the suggested configurations:


Normally, a pre-scan is run before each GE sequence.  One of the things that the pre-scan does is to re-measure the peak frequency corresponding to water. This in effect compensates for drift in the overall magnetic field strength (which may be due to heating which in turn is dependent on what pulse sequences you run).  But change in the magnetic field is exactly what we are trying to track using fieldmaps.  So, some fancy footwork is necessary to avoid re-measuring the peak frequency.
* T1w 1mm ax (3:22): T1-weighted, 1mm^3 voxel size, 3D Bravo, axial slices. A single scan gives good signal-to-noise quality. If you just want a basic, fast, axial T1 weighted scan, go with this.   


The strategy that Kendrick likes is this:
* T1w 1mm sag (3:43): T1-weighted, 1mm^3 voxel size, 3D Bravo, sagittal slices. A single scan gives good signal-to-noise quality. This is similar to the 1mm axial, but with sagittal slice orientation. Compared to axial, this orientation is slightly less efficient because you need a full phase FOV, but sagittal slices usually do better than axial with artifacts from large blood vessels (e.g., carotid artifacts land in non-brain regions rather than the temporal lobes) and with fat-shift artifacts, because the shifted scalp signal usually misses the brain while with axial it can sometimes overlap the occipital lobe gray matter, causing tissue segmentation problems.
# After completing the localizer, ASSET calibration, higher-order shim, and in-planes, we are ready to proceed to the actual functional data.
# Set up the EPI sequence and prescribe only one volume.  Then hit SCAN as usual. This will trigger the pre-scan and acquire one volume.  We want to trigger the pre-scan because the pre-scan includes other calibration routines that reduce ghosting, etc.
# Then, proceed to collect your actual data by sandwiching EPI runs within fieldmap acquisitions, like F1 / E1 / F2 / E2 / F3 / E3 / F4.  This ensures that you have a good estimate of the field throughout all of the EPI data.
# Importantly, when starting each EPI and each fieldmap, click Save Rx, then click Research->Download, then Manual Prep Scan.  This will open up a window.  Don't do anything and just click DONE.  Then click Prep Scan.  Then press the green button on the console keyboard to start the scan.  By using this procedure to start the scan, we avoid the pre-scan and therefore avoid the re-calibration of the peak frequency.


If for some reason, later in the session, you decide to acquire sequences other than fieldmaps and EPIs, you should allow the pre-scan to run as usual (by just hitting the SCAN button to scan). Of course, this will change the global constant describing the field strength.
* T1w 0.9mm sag (4:49) T1-weighted, 0.9mm^3 voxel size, 3D Bravo, sagittal slices. A single scan gives good signal-to-noise quality. As with the above scan, but a little higher spatial resolution. If you can afford to take 5 minutes for a T1 scan, this one is a great choice. This is our work-horse. Note: to get true .9 isotropic voxels, enter '23.04' for the FOV. The scanner GUI will display this as '23.0', but will store and use the full-precision that you type!


Also, if you for some reason change parameters of the EPI sequence (such as TR, TE, phase direction), you need to allow the pre-scan to run so that proper calibration can be done.  However, certain EPI parameters do not necessitate a pre-scan, like number of volumes to acquire and the phase-encode polarity (which is controlled through the CV variable pepolar).
* T1w 0.8mm sag (4:57 X 2): T1-weighted, 0.8mm^3 voxels, 3D Bravo, sagittal slices. Two scans (averaged in post-processing) are advised for good signal-to-noise quality. If you want to get better resolution, do two of these.


Admittedly, sandwiching every EPI run between fieldmaps is an aggressive (and paranoid) strategy --- each fieldmap takes about a minute to acquire. If you like, it may be okay to space the fieldmaps more sparsely, e.g. F1 / E1 / E2 / F2 / E3 / E4 / F3, depending on how long your EPI runs are.  Of course, this comes at the expense of having sub-optimal tracking of the field.
* T1w 0.7mm sag (5:41 X 3): T1-weighted, 0.7mm^3 voxels, 3D Bravo, sagittal slices. 3-4 scans (averaged in post-processing) are advised for good signal-to-noise quality. If you can afford the time, and make use of high-quality anatomical images, this is the sequence to use.


As an even less aggressive strategy, it is also conceivable to acquire only a single fieldmap (indeed, it appears that that's what most laboratories do, if anything at all) and also allow each EPI run to do the pre-scan (which avoids the cumbersome Manual Prep Scan procedure).  The hope here is that the bulk of the drift in the magnetic field can be captured by just a change in a global constant.  (To a first approximation, it does appear that the overall DC in the field is the biggest effect, but in data that I have looked at, there are additional components that can't be described by just a constant.)
===T2 weighted ===


'''Spiral fieldmap acquisition'''
* 3D T2 (5:03): T2-weighted, 0.8mm^3 voxel size, 3D Cube T2, sagittal slices. A single scan gives good signal-to-noise quality.


Atsushi has developed a spiral-based sequence for measuring fieldmaps, and the quality is quite good. Here are the parameters that Kendrick recommends for optimal quality:
* 3D T2 FLAIR (6:17): T2-weighted, 1 mm^3 voxel size, 3D Cube T2, sagittal slices. An additional inversion-recovery pulse is applied in the 3D T2 CUBE sequence to suppress the CSF signal in the T2 weighted images.
# First, set slice thickness.
 
# Then copy slices from the EPI (or in-plane) sequence.
* 3D T2 PROMO (5:42): T2-weighted, 0.8mm^3 voxel size, 3D Cube T2, sagittal slices. PROMO (PROspective MOtion correction) adjusts the scan parameters during the scan to prospectively correct for patient motion and thus reducing the image artifacts.
# 16-shot (16 spiral interleaves). The purpose is to minimize the readout time so as to minimize distortion and dropout (in combination with an appropriately short TE).
 
# 700 ms TR.  You could try to reduce this value to speed up acquisition. If the other parameters necessitate a longer TR, the sequence will silently use a longer TR and the scanner will scan past the on-screen time countdown. This is okay, just wait a few seconds.
=== T2w/PDw ===
# 54° flip. This is the Ernst angle for the 700 ms TR (assuming a T1 constant of 1333.33 ms).
 
# no SAT. In regions of bad field inhomogeneity, water will be off-resonance. So if you were to use a fat saturation pulse, you could destroy the water signal in these regions.  That is bad.  So, leave SAT off.
2D T2w/PDw FSE (4:25): A standard 2D T2-weighted scan. You also get a bonus proton-density scan. Note that the two datasets will be interleaved; you'll want to separate them in post-processing.
# 256 x 256.  This is a fairly high matrix size which will ensure high-resolution, high-quality field maps.
 
# 2 NEX.  Get two repetitions to ensure that the fieldmaps will have high SNR. If time is a consideration, you might try going down to 1 NEX.
=== Technical Notes ===
# 24.0 FOV. This is a large FOV to ensure that the entire head is completely covered in the in-plane dimensions. You could reduce, but be careful.
 
# 6 dummies to ensure we reach a steady-state.
In general, using a higher pixel bandwidth can help reduce chemical shift effects that push the fat signal from the scalp into the brain.
# 4.545 ms TE. This is 1/440Hz * 2. It is unclear whether saved protocols will save the precise TE value. So it is recommended that you manually type in 4.545 in each scan session. (After typing it in, copying and pasting that sequence does preserve the precise value.)
 
# map_deltaf 440. You must edit this CV variable after saving and downloading the spiral sequence.   (The purpose of the TE and map_deltaf values is to choose echo times that are matched to the difference between the precession frequencies of water and fat, so that the resulting fieldmaps will have minimal artifacts.)
The 3D Geometry Correction option uses a 3D correction for gradient non-linearity, over the 2D correction that is performed when the option is not checked. By including the slice direction in the correction, the resulting images are closer to geometric truth. The model used to represent gradient nonlinearity is the same as the 2D correction ("gradwarp") and it uses the same cubic interpolation function as the 2D correction.
# Note: it is very important that you get the TE and map_deltaf values right!  Otherwise, there will be fat-related artifacts in your fieldmaps.
 
# You will have to transfer the raw fieldmap data yourself (they do not get converted to DICOM format like data from the stock GE sequences).  The files are named like P39936.7.
== Functional imaging ==
 
=== BOLD EPI (Full brain) ===
 
BOLD EPI 2.9mm 2sec: gradient echo EPI, 2.9mm^3 voxel size, 45 slices (~13 cm), TR/TE 2s/30ms, 2x in-plane acceleration. This sequence gives you full coverage of the brain. The 2x in-plane acceleration reduces the EPI distortion. This is a standard sequence for fMRI scans.
 
=== BOLD EPI (High resolution, partial brain) ===
 
BOLD EPI 1.8mm 2sec (partial coverage): gradient echo EPI, 1.8mm^3 voxel size, 25 slices (~4.5 cm), TR/TE 2s/30ms, 2x in-plane acceleration. This sequence gives you partial coverage of the brain at a higher resolution. It is a good choice if you are interested in a particular part of the brain.
 
===Technical Notes ===
If your protocol has multiple long-duration functional scans, you may consider doing additional field map measurements between the functional scans to access any field drift. See the [[Improving EPI]] page for information on fixing some common image problems with EPI images.
 
There is a field map template protocol within the CNI/Head/CNI Example fMRI: Spiral fieldmap (0:27): 2D spiral, 1.75 x 1.75 x 2mm^3 voxel size. Copy the slice coverage of the BOLD scan. This scan generates a B0 field map in Hz (along with a magnitude image).
 
The optimal echo time (TE) for BOLD fMRI at 3T is 30ms, where the difference in T2* decay of oxy/deoxy hemoglobin gives the highest contrast in the measured MR signals between the oxy/deoxy-genated blood.
 
When doing BOLD fMRI, we prefer reading out the data at the optimal echo time quickly. When the TR (the repetition time) is shorter than the longitudinal relaxation time (T1) of the tissue of interest, we want to adjust the flip angle to optimize the SNR by maximizing the magnetization recovery along the z-axis (T1) during successive excitations of the same tissue. The optimal flip-angle is found by the Ernst equation:
 
''flip-angle = acos(exp(-TR/T1)) ''
 
[Note: this formula will return values in radians, which then need to be converted to degrees. Alternatively, if using Matlab, use the acosd function which will return degrees.]
 
* A typical T1 value for gray matter is (3T): 1.33 seconds (Kruger, et al, 2001). (At 1.5T, it is closer to 0.9 seconds.)
 
*Or use the following values for typical TRs at 3T:
 
{|style="border-collapse: collapse; border-width: 1px; border-style: solid; border-color: #000"
|-
|style="border-style: solid; border-width: 1px; text-align: right"| '''TR (s):'''
|style="border-style: solid; border-width: 1px; text-align: center"| 1
|style="border-style: solid; border-width: 1px; text-align: center"| 1.5
|style="border-style: solid; border-width: 1px; text-align: center"| 2
|style="border-style: solid; border-width: 1px; text-align: center"| 2.5
|style="border-style: solid; border-width: 1px; text-align: center"| 3
|style="border-style: solid; border-width: 1px; text-align: center"| 3.5
|style="border-style: solid; border-width: 1px; text-align: center"| 4
|style="border-style: solid; border-width: 1px; text-align: center"| 5
|style="border-style: solid; border-width: 1px; text-align: center"| 6
|style="border-style: solid; border-width: 1px; text-align: center"| 7
|-
|style="border-style: solid; border-width: 1px; text-align: right"| '''flip (deg):'''
|style="border-style: solid; border-width: 1px; text-align: center"| 61.9
|style="border-style: solid; border-width: 1px; text-align: center"| 71.1
|style="border-style: solid; border-width: 1px; text-align: center"| 77.2
|style="border-style: solid; border-width: 1px; text-align: center"| 81.2
|style="border-style: solid; border-width: 1px; text-align: center"| 84.0
|style="border-style: solid; border-width: 1px; text-align: center"| 85.9
|style="border-style: solid; border-width: 1px; text-align: center"| 87.2
|style="border-style: solid; border-width: 1px; text-align: center"| 88.7
|style="border-style: solid; border-width: 1px; text-align: center"| 89.4
|style="border-style: solid; border-width: 1px; text-align: center"| 89.7
|}
 
== Diffusion weighted imaging ==
 
=== DTI ===
* DTI 2mm b1000 60dir (9:21): 2mm^2 voxel size, 60-70 axial slices, b-value 1000, 60 diffusion directions.
 
=== HARDI ===
* DTI 2mm b2500 96dir (16:58): 2mm^2 voxel size, 60-70 axial slices, b-value 2500, 96 diffusion directions.
If you are pressed for time, you can drop the b-value to 2000 and/or reduce the number of directions to 80:
* DTI 2mm b2000 96dir (16:26): 2mm^2 voxel size, 60-70 axial slices, b-value 2000, 96 diffusion directions.
* DTI 2mm b2000 80dir (12:37): 2mm^2 voxel size, 60-70 axial slices, b-value 2000, 80 diffusion directions.
 
=== Technical Notes ===
Diffusion imaging at the CNI uses a modified version of GE's DW-EPI sequence. The sequence was modified so that for dual-spin-echo scans, the polarity of the second 180 degree pulse is inverted relative to the first 180. This causes off-resonance signal from fat to get defocused and thus help reduce fat-shift artifacts (See Sarlls et. al. Robust fat suppression at 3T in
high-resolution diffusion-weighted single-shot echo-planar imaging of human brain. MRM 2011, PubMed PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21604298 21604298] and Reese et. al. Reduction of eddy-current-induced distortion in diffusion MRI using a twice-refocused spin echo. MRM 2003, PubMed PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12509835 12509835]).
 
To decide on an optimal High Angular Resolution Diffusion Imaging (HARDI) acquisition protocol, see:
* [http://www.ncbi.nlm.nih.gov/pubmed/19603409 White and Dale (2009)] Optimal diffusion MRI acquisition for fiber orientation density estimation: an analytic approach. HBM. (Calculated optimal b-values for maximum FOD estimation efficiency with SH expansion orders of L = 2, 4, 6, and 8 to be approximately b = 1,500, 3,000, 4,600, and 6,200 s/mm^2; demonstrated how scanner-specific hardware limitations generally lead to optimal b-values that are slightly lower than the ideal b-values.)
* [http://www.ncbi.nlm.nih.gov/pubmed/18583153 Tournier et al. (2008)] Resolving crossing fibres using constrained spherical deconvolution: validation using diffusion-weighted imaging phantom data. NeuroImage. (For a 45 degrees crossing, the minimum b-value required to resolve the fibre orientations was ... 2000 s/mm^2 for CSD, and 1000 s/mm^2 for super-CSD.)
* [http://www.ncbi.nlm.nih.gov/pubmed/17379540 Tournier et al. (2007)] Robust determination of the fibre orientation distribution in diffusion MRI: non-negativity constrained super-resolved spherical deconvolution. NeuroImage.
 
HARDI data analysis tools include Camino, dipy, mrTrix etc.
 
We use a modified version of the stock GE DWI-EPI pulse sequence. The resulting dicoms contain the diffusion parameters in these fields:
* b-value (in sec/mm^2): 0043 1039 (GEMS_PARMS_01 block, item 1039)
* gradient direction: [0019 10bb, 0019 10bc, 0019 10bd] (GEMS_ACQU_01 block, items 10bb - 10bd)
In mrTrix (mapper.cpp), the following code is used to convert the dicom gradient values to the saved gradient directions:
 
  // M is the image transform
M(0,0) = -image.orientation_x[0];
M(1,0) = -image.orientation_x[1];
M(2,0) =  image.orientation_x[2];
M(0,1) = -image.orientation_y[0];
M(1,1) = -image.orientation_y[1];
M(2,1) =  image.orientation_y[2];
  M(0,2) = -image.orientation_z[0];
M(1,2) = -image.orientation_z[1];
M(2,2) =  image.orientation_z[2];
  M(0,3) = -image.position_vector[0];
M(1,3) = -image.position_vector[1];
M(2,3) =  image.position_vector[2];
M(3,0) = 0.0; M(3,1) = 0.0; M(3,2) = 0.0; M(3,3) = 1.0;
H.DW_scheme(s, 0) = M(0,0)*d[0] + M(0,1)*d[1] - M(0,2)*d[2];
H.DW_scheme(s, 1) = M(1,0)*d[0] + M(1,1)*d[1] - M(1,2)*d[2];
  H.DW_scheme(s, 2) = M(2,0)*d[0] + M(2,1)*d[1] - M(2,2)*d[2];
 
If you get the data from the CNI Neurobiological Image Management System (NIMS), then the b-values and b-vectors have already been extracted for you and are provided along with the NIFTI file containing your data. These three files (the NIFTI, bvals, and bvecs files) can be send directly into most diffusion data analysis packages, such as the Stanford Vita Lab [[http://vistalab.stanford.edu/newlm/index.php/MrDiffusion mrDiffusion]] or FSL's [[http://www.fmrib.ox.ac.uk/fsl/fdt/index.html FDT]]. The b-values file contains a set of numbers (one for each acquired volume) that describe the b-value of the corresponding volume. The b-vecs file contains a triplet of numbers for each acquired volume, describing the diffusion-weighting direction for the corresponding volume. E.g., if you run our 60-direction scan, you will get 6 non-DW volumes followed by 60-DW volumes. Thus, you nifti file will contain 66 volumes. The b-vals file will contain 66 numbers (six 0's, fllowed by 60 1000's) and the b-vecs files will contain 66 triplets describing the DW directions for each volume (the triplets for the first 6 non-DW volumes are meaningless and can be ignored).
 
=Simultaneous Multi-Slice (SMS)=
The CNI, in collaboration with GE, implemented [http://www.sciencedirect.com/science/article/pii/S1090780713000311 simultaneous multi-slice EPI] (also known as multiband EPI). GE has integrated the SMS EPI into its product software platform, and since CNI's scanner upgrade to the UHP system, the SMS sequence is available as part of the GE product sequences, called the Hyperband. The Hyperband option is available for both BOLD EPI and diffusion EPI.  
 
Previously CNI has provided the SMS sequence using our research PSD, the one we referred to as the "mux" sequence. We recommend everyone who has been using the "mux" sequence to transition to the Hyperband sequence. For a comparison of features and performances between the "mux" and Hyperband sequence, please see this CNI blog [http://cni.stanford.edu/hyperband-transition/ Hyperband transition]. More information about the legacy "mux" sequence is described on the [[MUX EPI]] page.
 
== SMS fMRI ==
The Hyperband sequence uses a calibration process that is integrated in the prescan. It is not necessary to set up a separate calibration scan or account for additional calibration volumes in the EPI time series. The calibration data is not saved in the final images. By default all the volumes in the EPI time series are reconstructed and saved in the final images, so the number of volumes in NIFTI is exactly the same amount as specified in the protocol (in the Multi-Phase page). However, the first few volumes in the time series may have different intensity because the spin magnetization has not yet reached steady state. In the BOLD analysis it may be necessary to discard the first few volumes in order to get to the steady state. Alternatively, there is an option in the Hyperband sequence to allow users to specify a number of dummy volumes, in which case the scanner will not reconstruct the first few volumes, but the scan timing is still the same, i.e. data acquisition starts right after the scan trigger.  
 
=== BOLD EPI ===
* Hyperband 6, voxel size 2.4mm^3, FOV 21.6cm, number of slices 60, TR 710ms (scan protocol in the Connectome project)
* Hyperband 6, voxel size 1.8mm^3, FOV 23.0cm, number of slices 81, TR 1386ms
* Hyperband 8, voxel size 3.0mm^3, FOV 22.2cm, number of slices 48, TR 415ms
* Hyperband 8, voxel size 2.0mm^3, FOV 22.0cm, number of slices 72, TR 760ms
 
=== Multi-echo EPI ===
* Hyperband 3, 2x in-plane acceleration, 3 EPI echoes, voxel size 2.8mm^3, FOV 22.4cm, number of slices 51, TR 1.49s, shortest TE 14.6ms, TE interval 23ms
 
== SMS DWI ==
For SMS diffusion scans we generally recommend 2x to 3x slice acceleration, which will bring down the scan time by 2 to 3 times while maintaining the SNR of the diffusion weighted images. Partial Fourier acquisition is usually used to keep the TE as short as possible. The in-plane acceleration in addition to the slice acceleration is not always recommended because even though it can further reduce the EPI distortion but the SNR loss can be harmful for diffusion model fitting.
 
Diffusion Spectrum Imaging (DSI) ([http://onlinelibrary.wiley.com/doi/10.1002/mrm.20642/full Magn. Reson. Med., 2005, 54: 1377–1386]) and multi-shell diffusion ([http://onlinelibrary.wiley.com/doi/10.1002/mrm.24736/full Magn. Reson. Med., 2013, 69: 1534–1540]) scans can be realized by designing gradient tables that specify direction and amplitude of the b-vectors. We set up a several customized gradient tables that are optimized for DTI, HARDI, 2 or 3-shell diffusion scans. Consult with us if you would like to set up your own diffusion gradient scheme.
 
=== HARDI ===
* DTI 80dir 2mm (4:45): SMS factor 3, axial slices, 2mm^3 voxel size, number of slices 69, b-value 2500, 80 diffusion directions, 8 b=0 images
* DTI 96dir 2mm (5:50): SMS factor 3, axial slices, 2mm^3 voxel size, number of slices 69, b-value 3000, 96 diffusion directions, 10 b=0 images
 
=== Multi-shell diffusion ===
* DTI g79/81 b3k 2-shell (4:33+4:40): 2-shell with 10 b=0 images, 75 directions at b=1500, 75 directions at b=3000. SMS factor 4, voxel size 1.5mm^3, number of slices 84 (scan protocol in the Connectome project)
* DTI g103 b2k 2-shell (4:50): 2-shell with 9 b=0 images, 30 directions at b=700, 64 directions at b=2000. SMS factor 3, 2x in-plane acceleration, voxel size 2mm^3, number of slices 75
* DTI g150 b3k 3-shell (6:15): 3-shell with 10 b=0 images, 30 direction at b=1000, 45 direction at b=2000, 65 direction at b=3000. SMS factor 3, 2x in-plane acceleration, voxel size 2mm^3, number of slices 63
 
= Scientific Protocols for Tissue and Chemistry =
 
== Quantitative MR ==
These template protocols make quantitative measurements of MR parameters (e.g. T1 in seconds, and proton density (PD) as a fraction of the voxel) of brain tissue.  Some 1 - PD is called the macromolecular tissue volume.
 
=== T1 map ===
The SS-SMS T1 scan is a quantitative T1 scan using slice-shuffled inversion-recovery SMS EPI sequence. This scan gives you a T1 measurement at 2mm isotropic resolution in a minimum time. It uses in-plane acceleration therefore it's not necessary to run a separate pe1 scan for distortion correction unless you have enough time. For processing the NIFTI file from either pe0 or pe1 scan to get the T1 map, you can use [http://github.com/cni/t1fit/blob/master/t1_fitter.py this Python script]. If you acquired both pe0 and pe1, then you can use [http://github.com/cni/t1fit/blob/master/t1fit_unwarp.py this script] to process both NIFTI files to get the T1 map -- this includes an extra step for distortion correction using FSL's TOPUP before fitting the T1 relaxation.  
 
* SS-SMS T1 pe0 (pe1) (2:03): Gradient echo IR EPI, 2mm^3 voxel size, number of muxed slices 25 (75 unmuxed slices, 15cm), SMS factor 3, 2x in-plane acceleration, TR 3s.
 
=== T1 map + PD map ===
The four SPGR scans, together with the four IR EPI scans, are set up for calculating T1 and PD maps using the [http://github.com/mezera/mrQ mrQ analysis package]. If you want a high resolution T1 map, or if you are interested in getting PD in addition to T1, then you should use this group of scans.
 
* SPGR 1mm 30(4/10/20) deg (5:19 X 4): 3D SPGR, 1mm^3 voxel size, flip angle 30/4/10/20. The first scan should be run with Auto Prescan + Scan, and the following three should be run using Manual Prescan (do not change any parameters) + Scan.
 
* IR EPI TI=50(400/1200/2400) (1:15 X 4): Gradient echo IR EPI, 1.875 x 1.875 x 4mm^3 voxel size, 2x in-plane acceleration. The first scan should be run with Auto Prescan + Scan, and the following three should be run using Manual Prescan (do not change any parameters) + Scan.
 
Note that you could also choose to use only the four IR EPI scans to get a quantitative T1 map at a lower resolution. The working principle and model fitting procedure is explained [http://www-mrsrl.stanford.edu/~jbarral/t1map.html here].
 
== Spectroscopy ==
In-vivo spectroscopy sequences and analysis methods available and used at CNI are described [[GABA spectro | on this CNI spectroscopy page]].
 
= Additional information (deprecated) =
== Device specific processing ==
The [[GE Processing | General Electric processing]] includes various steps that can influence the signal-to-noise of your data.  We explain what we have learned about this and how to control it in the [[GE Processing]] page.
 
== Technical notes ==
* [[media:bob_spatialRes_111216.pdf|Slides on spatial resolution]] from CNI tutorial
* [[MR Signal Equations]]
 
== Session Running Script ==
 
We advise you to put together a session running script that outlines set up of the scanner and peripherals and positioning of and communications with the participant. You can find an example [[media:Session_Running_Script.pdf|here]] (courtesy of Nanna Notthoff, Carstensen Lab).
 
== CNI's Quality Assurance protocol ==
Weekly QA scans include:
# BOLD EPI sequence (analyze mean and variance over time)
# DW EPI sequence (analyze eddy current distortion stability)
# Spiral field map (analyze long-term B0 stability)
All QA scans are done on the fBIRN agar phantom. The phantom is positioned in the same orientation with the same padding each week. The landmark must be set to the same. The Rx should be not touched (use the same stored Rx). We should do HO shim and set the shim VOI to exactly cover the sphere.

Latest revision as of 17:35, 23 August 2023

This page offers advice about how to set up your scan protocols and save the information. The wiki pages take you through the template protocols we think are most widely used. These protocols can be found on the the scanner console, saved under “CNI/head” within the protocol pool.

Screenshots to remind you about how to set specific MRI protocols can be found on the page Setting up protocols

General

Setting up an MR scan protocol

A basic MR scan session usually starts with the following scans:

  • Localizer - a 3-plane localizer or 'scout' scan meant to find the subject's head. It is also be used for prescription for the subsequent scans. Doing some sort of localizer is necessary, and the '3planeloc SSFSE' (single shot fast spin echo) is the standard work-horse used by most CNI users.
  • Anatomical - usually a 3D T1-weighted scan at 0.9mm or 1mm isotropic resolution. It is essential for image alignment and anatomical analysis. More choices of anatomical scans are listed in the Anatomical imaging section.
  • ASSET calibration - a calibration scan for parallel imaging. It should be run before any scans that will use ASSET, such as GE's conventional fMRI and diffusion scans.
  • Higher-order shim - measures the magnetic field inhomogeneity and corrects it with polynomial gradients up to 2nd order. It should be run after ASSET and before fieldmap, fMRI or diffusion scans.
  • Field map - measures the magnetic field inhomogeneity that cannot be corrected by the shim and saves the inhomogeneity in a field map. It should be run immediately before or after the fMRI scan.

At this point you will want to add a number of functional scans, diffusion scans or other type of scans based on your experiment. In the next section we describe templates for different categories of MRI protocols. The protocol templates are organized by category. One set is based on conventional multislice (2D) or 3D methods, a second set is based on the new simultaneous multislice (SMS) protocols (also called mux or multiband), and a third set are some special methods (spectroscopy and qMRI).

You can get help in customizing the parameters from the CNI staff (ask Hua, Adam, or Laima).

Saving your protocol parameters

Save screen-shots

At the GE console, you can save screen shots of the GE interface to show the main parameters that you have set in a protocol. Just get to the screen that you want to save, then press the 'Prnt Scrn' button on the keyboard. A little dialog will show up. You can choose to print, which will print on paper to the Laser printer in the control room. However, we strongly suggest that you save some trees and the toxic ink chemicals by saving a digital copy instead. To do this, type ina reasonable name in the filename field (default is 'screen') and hit the 'PNG" button. A PNG image will then magically appear in the 'screensaves' folder on the linux machine next to the console (cnirt). From there, you can email the images to yourself. Or, even better, create your own personal wiki page here that describes your protocol (just log in with your SUNet ID) and put the images in there. Then, you will always have them available when needed! THis is also a great way to share protocol information with your colleagues.

Get a PDF of all protocol parameters

You can get a complete PDF of all your protocol info with a few clicks of the mouse. It's not quite as easy as a screensave, so we outline the procedure here. Note - There is a change on figure 4 - The pdf file will now appear with some viewing options at the top of the pdf file. By clicking on the 4th option from the right (a square with three parallel lines) the drop down menu will display a "save a copy" option which will result in the pdf being saved in the screensaves folder on the Linux machine (voxel2) next to the scanner.

  • Click the "Protocol Exchange" button under the Image Management tab.
    Click the "Protocol Exchange" button under the Image Management tab.
  • Select "Export Mode" and click OK in the dialog that comes up.
    Select "Export Mode" and click OK in the dialog that comes up.
  • Find your protocol in the next dialog, drag it to the "Protocol Selection" panel, and make sure it is selected. Then press the "preview" button.
    Find your protocol in the next dialog, drag it to the "Protocol Selection" panel, and make sure it is selected. Then press the "preview" button.
  • You'll then see the PDF of your protocol. Right-click anywhere within the pdf and select "Save as..." from the drop-down menu.
    You'll then see the PDF of your protocol. Right-click anywhere within the pdf and select "Save as..." from the drop-down menu.
  • Type the path and filename. Be sure that the path is /usr/g/mrraw/screensaves/ so it'll magically appear in the "screensaves" directory on the linux box.
    Type the path and filename. Be sure that the path is /usr/g/mrraw/screensaves/ so it'll magically appear in the "screensaves" directory on the linux box.

MRI protocol templates

The CNI has stored example protocols for anatomical, fMRI, diffusion, spectroscopy and quantitative MR scans (named as "CNI Examples", stored under "CNI / Head"). Depending on the user's needs, there are several ways to run a scan session. The stored protocols are meant to be used as a 'menu' from which you select the sequence that you want, based on your needs. While there are many variations stored there, here we just highlight a couple of the most common versions. A detailed list of all parameters for all scans can be found in the PDF files for each protocol. Some suggested ways of selecting from and set up these scans for your own scan session are described below.

Moving protocols from CNI to Lucas

If you plan to transfer scan protocols from the CNI to Lucas Center, please contact Hua and follow the steps below:

  • Let CNI staff know the (a) name of the protocol(s) to transfer and (b) which Lucas scanner. It would be useful if you could include a list of scans in your protocol too. We will help transfer the protocol files over to Lucas.
  • If your protocol contains pulse sequences provided by researchers outside CNI, then please let them know about the transfer so that they can prepare the sequences for you at Lucas. For example, if you run any spectroscopy sequences, then please let Dr Meng Gu know about the transfer plan.
  • Follow up with Lucas staff about setting up peripheral devices, e.g. response box, scanner trigger, visual display, physio recording, etc. The visual display at both Lucas scanners uses a projector and a screen mounted on the head coil. Another thing to keep in mind is that Lucas scanners do not send out scan triggers in the same way as the CNI scanner does, so it’s preferred to let the stimulation program trigger the scanner by writing out a byte through the usb-serial port. Lucas also provides their version of the functional sequences that send out triggers to the computer, if you prefer to let the scanner trigger your stimulation. For more details please seek advice from the Lucas staff.
  • The Lucas center has its own instance of Flywheel lucascenter.flywheel.io. Prior to scanning at Lucas, please be sure to coordinate with Tom Brosnan, or Michael Perry, to have your group’s accounts and projects configured. Michael can help you make sure your projects have the correct gear rules configured to process your data, which is an important consideration to maintain consistency across the two sites. As a good first approximation you can map existing project gear rules at CNI to your new projects at Lucas. Our goal is to make the same gears available at Lucas as are available at CNI. This is a work in progress.

Conventional imaging

Anatomical imaging

T1 weighted

All the suggested T1-weighted scans use GE's "BRAVO" sequence. It is an IR-prep, fast SPGR sequence with parameters tuned to optimize brain tissue contrast. Unless you have good reason to do so, you probably don't want to play with any parameters other than slice orientation, voxel size, and bandwidth. And for those, most users just pick one of the suggested configurations:

  • T1w 1mm ax (3:22): T1-weighted, 1mm^3 voxel size, 3D Bravo, axial slices. A single scan gives good signal-to-noise quality. If you just want a basic, fast, axial T1 weighted scan, go with this.
  • T1w 1mm sag (3:43): T1-weighted, 1mm^3 voxel size, 3D Bravo, sagittal slices. A single scan gives good signal-to-noise quality. This is similar to the 1mm axial, but with sagittal slice orientation. Compared to axial, this orientation is slightly less efficient because you need a full phase FOV, but sagittal slices usually do better than axial with artifacts from large blood vessels (e.g., carotid artifacts land in non-brain regions rather than the temporal lobes) and with fat-shift artifacts, because the shifted scalp signal usually misses the brain while with axial it can sometimes overlap the occipital lobe gray matter, causing tissue segmentation problems.
  • T1w 0.9mm sag (4:49) T1-weighted, 0.9mm^3 voxel size, 3D Bravo, sagittal slices. A single scan gives good signal-to-noise quality. As with the above scan, but a little higher spatial resolution. If you can afford to take 5 minutes for a T1 scan, this one is a great choice. This is our work-horse. Note: to get true .9 isotropic voxels, enter '23.04' for the FOV. The scanner GUI will display this as '23.0', but will store and use the full-precision that you type!
  • T1w 0.8mm sag (4:57 X 2): T1-weighted, 0.8mm^3 voxels, 3D Bravo, sagittal slices. Two scans (averaged in post-processing) are advised for good signal-to-noise quality. If you want to get better resolution, do two of these.
  • T1w 0.7mm sag (5:41 X 3): T1-weighted, 0.7mm^3 voxels, 3D Bravo, sagittal slices. 3-4 scans (averaged in post-processing) are advised for good signal-to-noise quality. If you can afford the time, and make use of high-quality anatomical images, this is the sequence to use.

T2 weighted

  • 3D T2 (5:03): T2-weighted, 0.8mm^3 voxel size, 3D Cube T2, sagittal slices. A single scan gives good signal-to-noise quality.
  • 3D T2 FLAIR (6:17): T2-weighted, 1 mm^3 voxel size, 3D Cube T2, sagittal slices. An additional inversion-recovery pulse is applied in the 3D T2 CUBE sequence to suppress the CSF signal in the T2 weighted images.
  • 3D T2 PROMO (5:42): T2-weighted, 0.8mm^3 voxel size, 3D Cube T2, sagittal slices. PROMO (PROspective MOtion correction) adjusts the scan parameters during the scan to prospectively correct for patient motion and thus reducing the image artifacts.

T2w/PDw

2D T2w/PDw FSE (4:25): A standard 2D T2-weighted scan. You also get a bonus proton-density scan. Note that the two datasets will be interleaved; you'll want to separate them in post-processing.

Technical Notes

In general, using a higher pixel bandwidth can help reduce chemical shift effects that push the fat signal from the scalp into the brain.

The 3D Geometry Correction option uses a 3D correction for gradient non-linearity, over the 2D correction that is performed when the option is not checked. By including the slice direction in the correction, the resulting images are closer to geometric truth. The model used to represent gradient nonlinearity is the same as the 2D correction ("gradwarp") and it uses the same cubic interpolation function as the 2D correction.

Functional imaging

BOLD EPI (Full brain)

BOLD EPI 2.9mm 2sec: gradient echo EPI, 2.9mm^3 voxel size, 45 slices (~13 cm), TR/TE 2s/30ms, 2x in-plane acceleration. This sequence gives you full coverage of the brain. The 2x in-plane acceleration reduces the EPI distortion. This is a standard sequence for fMRI scans.

BOLD EPI (High resolution, partial brain)

BOLD EPI 1.8mm 2sec (partial coverage): gradient echo EPI, 1.8mm^3 voxel size, 25 slices (~4.5 cm), TR/TE 2s/30ms, 2x in-plane acceleration. This sequence gives you partial coverage of the brain at a higher resolution. It is a good choice if you are interested in a particular part of the brain.

Technical Notes

If your protocol has multiple long-duration functional scans, you may consider doing additional field map measurements between the functional scans to access any field drift. See the Improving EPI page for information on fixing some common image problems with EPI images.

There is a field map template protocol within the CNI/Head/CNI Example fMRI: Spiral fieldmap (0:27): 2D spiral, 1.75 x 1.75 x 2mm^3 voxel size. Copy the slice coverage of the BOLD scan. This scan generates a B0 field map in Hz (along with a magnitude image).

The optimal echo time (TE) for BOLD fMRI at 3T is 30ms, where the difference in T2* decay of oxy/deoxy hemoglobin gives the highest contrast in the measured MR signals between the oxy/deoxy-genated blood.

When doing BOLD fMRI, we prefer reading out the data at the optimal echo time quickly. When the TR (the repetition time) is shorter than the longitudinal relaxation time (T1) of the tissue of interest, we want to adjust the flip angle to optimize the SNR by maximizing the magnetization recovery along the z-axis (T1) during successive excitations of the same tissue. The optimal flip-angle is found by the Ernst equation: 

flip-angle = acos(exp(-TR/T1))

[Note: this formula will return values in radians, which then need to be converted to degrees. Alternatively, if using Matlab, use the acosd function which will return degrees.]

  • A typical T1 value for gray matter is (3T): 1.33 seconds (Kruger, et al, 2001). (At 1.5T, it is closer to 0.9 seconds.)
  • Or use the following values for typical TRs at 3T:
TR (s): 1 1.5 2 2.5 3 3.5 4 5 6 7
flip (deg): 61.9 71.1 77.2 81.2 84.0 85.9 87.2 88.7 89.4 89.7

Diffusion weighted imaging

DTI

  • DTI 2mm b1000 60dir (9:21): 2mm^2 voxel size, 60-70 axial slices, b-value 1000, 60 diffusion directions.

HARDI

  • DTI 2mm b2500 96dir (16:58): 2mm^2 voxel size, 60-70 axial slices, b-value 2500, 96 diffusion directions.

If you are pressed for time, you can drop the b-value to 2000 and/or reduce the number of directions to 80:

  • DTI 2mm b2000 96dir (16:26): 2mm^2 voxel size, 60-70 axial slices, b-value 2000, 96 diffusion directions.
  • DTI 2mm b2000 80dir (12:37): 2mm^2 voxel size, 60-70 axial slices, b-value 2000, 80 diffusion directions.

Technical Notes

Diffusion imaging at the CNI uses a modified version of GE's DW-EPI sequence. The sequence was modified so that for dual-spin-echo scans, the polarity of the second 180 degree pulse is inverted relative to the first 180. This causes off-resonance signal from fat to get defocused and thus help reduce fat-shift artifacts (See Sarlls et. al. Robust fat suppression at 3T in high-resolution diffusion-weighted single-shot echo-planar imaging of human brain. MRM 2011, PubMed PMID: 21604298 and Reese et. al. Reduction of eddy-current-induced distortion in diffusion MRI using a twice-refocused spin echo. MRM 2003, PubMed PMID: 12509835).

To decide on an optimal High Angular Resolution Diffusion Imaging (HARDI) acquisition protocol, see:

  • White and Dale (2009) Optimal diffusion MRI acquisition for fiber orientation density estimation: an analytic approach. HBM. (Calculated optimal b-values for maximum FOD estimation efficiency with SH expansion orders of L = 2, 4, 6, and 8 to be approximately b = 1,500, 3,000, 4,600, and 6,200 s/mm^2; demonstrated how scanner-specific hardware limitations generally lead to optimal b-values that are slightly lower than the ideal b-values.)
  • Tournier et al. (2008) Resolving crossing fibres using constrained spherical deconvolution: validation using diffusion-weighted imaging phantom data. NeuroImage. (For a 45 degrees crossing, the minimum b-value required to resolve the fibre orientations was ... 2000 s/mm^2 for CSD, and 1000 s/mm^2 for super-CSD.)
  • Tournier et al. (2007) Robust determination of the fibre orientation distribution in diffusion MRI: non-negativity constrained super-resolved spherical deconvolution. NeuroImage.

HARDI data analysis tools include Camino, dipy, mrTrix etc.

We use a modified version of the stock GE DWI-EPI pulse sequence. The resulting dicoms contain the diffusion parameters in these fields:

  • b-value (in sec/mm^2): 0043 1039 (GEMS_PARMS_01 block, item 1039)
  • gradient direction: [0019 10bb, 0019 10bc, 0019 10bd] (GEMS_ACQU_01 block, items 10bb - 10bd)

In mrTrix (mapper.cpp), the following code is used to convert the dicom gradient values to the saved gradient directions: 

// M is the image transform
M(0,0) = -image.orientation_x[0];
M(1,0) = -image.orientation_x[1];
M(2,0) =  image.orientation_x[2];
M(0,1) = -image.orientation_y[0];
M(1,1) = -image.orientation_y[1];
M(2,1) =  image.orientation_y[2];
M(0,2) = -image.orientation_z[0];
M(1,2) = -image.orientation_z[1];
M(2,2) =  image.orientation_z[2];
M(0,3) = -image.position_vector[0];
M(1,3) = -image.position_vector[1];
M(2,3) =  image.position_vector[2];
M(3,0) = 0.0; M(3,1) = 0.0; M(3,2) = 0.0; M(3,3) = 1.0;
H.DW_scheme(s, 0) = M(0,0)*d[0] + M(0,1)*d[1] - M(0,2)*d[2];
H.DW_scheme(s, 1) = M(1,0)*d[0] + M(1,1)*d[1] - M(1,2)*d[2];
H.DW_scheme(s, 2) = M(2,0)*d[0] + M(2,1)*d[1] - M(2,2)*d[2];

If you get the data from the CNI Neurobiological Image Management System (NIMS), then the b-values and b-vectors have already been extracted for you and are provided along with the NIFTI file containing your data. These three files (the NIFTI, bvals, and bvecs files) can be send directly into most diffusion data analysis packages, such as the Stanford Vita Lab [mrDiffusion] or FSL's [FDT]. The b-values file contains a set of numbers (one for each acquired volume) that describe the b-value of the corresponding volume. The b-vecs file contains a triplet of numbers for each acquired volume, describing the diffusion-weighting direction for the corresponding volume. E.g., if you run our 60-direction scan, you will get 6 non-DW volumes followed by 60-DW volumes. Thus, you nifti file will contain 66 volumes. The b-vals file will contain 66 numbers (six 0's, fllowed by 60 1000's) and the b-vecs files will contain 66 triplets describing the DW directions for each volume (the triplets for the first 6 non-DW volumes are meaningless and can be ignored).

Simultaneous Multi-Slice (SMS)

The CNI, in collaboration with GE, implemented simultaneous multi-slice EPI (also known as multiband EPI). GE has integrated the SMS EPI into its product software platform, and since CNI's scanner upgrade to the UHP system, the SMS sequence is available as part of the GE product sequences, called the Hyperband. The Hyperband option is available for both BOLD EPI and diffusion EPI.

Previously CNI has provided the SMS sequence using our research PSD, the one we referred to as the "mux" sequence. We recommend everyone who has been using the "mux" sequence to transition to the Hyperband sequence. For a comparison of features and performances between the "mux" and Hyperband sequence, please see this CNI blog Hyperband transition. More information about the legacy "mux" sequence is described on the MUX EPI page.

SMS fMRI

The Hyperband sequence uses a calibration process that is integrated in the prescan. It is not necessary to set up a separate calibration scan or account for additional calibration volumes in the EPI time series. The calibration data is not saved in the final images. By default all the volumes in the EPI time series are reconstructed and saved in the final images, so the number of volumes in NIFTI is exactly the same amount as specified in the protocol (in the Multi-Phase page). However, the first few volumes in the time series may have different intensity because the spin magnetization has not yet reached steady state. In the BOLD analysis it may be necessary to discard the first few volumes in order to get to the steady state. Alternatively, there is an option in the Hyperband sequence to allow users to specify a number of dummy volumes, in which case the scanner will not reconstruct the first few volumes, but the scan timing is still the same, i.e. data acquisition starts right after the scan trigger.

BOLD EPI

  • Hyperband 6, voxel size 2.4mm^3, FOV 21.6cm, number of slices 60, TR 710ms (scan protocol in the Connectome project)
  • Hyperband 6, voxel size 1.8mm^3, FOV 23.0cm, number of slices 81, TR 1386ms
  • Hyperband 8, voxel size 3.0mm^3, FOV 22.2cm, number of slices 48, TR 415ms
  • Hyperband 8, voxel size 2.0mm^3, FOV 22.0cm, number of slices 72, TR 760ms

Multi-echo EPI

  • Hyperband 3, 2x in-plane acceleration, 3 EPI echoes, voxel size 2.8mm^3, FOV 22.4cm, number of slices 51, TR 1.49s, shortest TE 14.6ms, TE interval 23ms

SMS DWI

For SMS diffusion scans we generally recommend 2x to 3x slice acceleration, which will bring down the scan time by 2 to 3 times while maintaining the SNR of the diffusion weighted images. Partial Fourier acquisition is usually used to keep the TE as short as possible. The in-plane acceleration in addition to the slice acceleration is not always recommended because even though it can further reduce the EPI distortion but the SNR loss can be harmful for diffusion model fitting.

Diffusion Spectrum Imaging (DSI) (Magn. Reson. Med., 2005, 54: 1377–1386) and multi-shell diffusion (Magn. Reson. Med., 2013, 69: 1534–1540) scans can be realized by designing gradient tables that specify direction and amplitude of the b-vectors. We set up a several customized gradient tables that are optimized for DTI, HARDI, 2 or 3-shell diffusion scans. Consult with us if you would like to set up your own diffusion gradient scheme.

HARDI

  • DTI 80dir 2mm (4:45): SMS factor 3, axial slices, 2mm^3 voxel size, number of slices 69, b-value 2500, 80 diffusion directions, 8 b=0 images
  • DTI 96dir 2mm (5:50): SMS factor 3, axial slices, 2mm^3 voxel size, number of slices 69, b-value 3000, 96 diffusion directions, 10 b=0 images

Multi-shell diffusion

  • DTI g79/81 b3k 2-shell (4:33+4:40): 2-shell with 10 b=0 images, 75 directions at b=1500, 75 directions at b=3000. SMS factor 4, voxel size 1.5mm^3, number of slices 84 (scan protocol in the Connectome project)
  • DTI g103 b2k 2-shell (4:50): 2-shell with 9 b=0 images, 30 directions at b=700, 64 directions at b=2000. SMS factor 3, 2x in-plane acceleration, voxel size 2mm^3, number of slices 75
  • DTI g150 b3k 3-shell (6:15): 3-shell with 10 b=0 images, 30 direction at b=1000, 45 direction at b=2000, 65 direction at b=3000. SMS factor 3, 2x in-plane acceleration, voxel size 2mm^3, number of slices 63

Scientific Protocols for Tissue and Chemistry

Quantitative MR

These template protocols make quantitative measurements of MR parameters (e.g. T1 in seconds, and proton density (PD) as a fraction of the voxel) of brain tissue. Some 1 - PD is called the macromolecular tissue volume.

T1 map

The SS-SMS T1 scan is a quantitative T1 scan using slice-shuffled inversion-recovery SMS EPI sequence. This scan gives you a T1 measurement at 2mm isotropic resolution in a minimum time. It uses in-plane acceleration therefore it's not necessary to run a separate pe1 scan for distortion correction unless you have enough time. For processing the NIFTI file from either pe0 or pe1 scan to get the T1 map, you can use this Python script. If you acquired both pe0 and pe1, then you can use this script to process both NIFTI files to get the T1 map -- this includes an extra step for distortion correction using FSL's TOPUP before fitting the T1 relaxation.

  • SS-SMS T1 pe0 (pe1) (2:03): Gradient echo IR EPI, 2mm^3 voxel size, number of muxed slices 25 (75 unmuxed slices, 15cm), SMS factor 3, 2x in-plane acceleration, TR 3s.

T1 map + PD map

The four SPGR scans, together with the four IR EPI scans, are set up for calculating T1 and PD maps using the mrQ analysis package. If you want a high resolution T1 map, or if you are interested in getting PD in addition to T1, then you should use this group of scans.

  • SPGR 1mm 30(4/10/20) deg (5:19 X 4): 3D SPGR, 1mm^3 voxel size, flip angle 30/4/10/20. The first scan should be run with Auto Prescan + Scan, and the following three should be run using Manual Prescan (do not change any parameters) + Scan.
  • IR EPI TI=50(400/1200/2400) (1:15 X 4): Gradient echo IR EPI, 1.875 x 1.875 x 4mm^3 voxel size, 2x in-plane acceleration. The first scan should be run with Auto Prescan + Scan, and the following three should be run using Manual Prescan (do not change any parameters) + Scan.

Note that you could also choose to use only the four IR EPI scans to get a quantitative T1 map at a lower resolution. The working principle and model fitting procedure is explained here.

Spectroscopy

In-vivo spectroscopy sequences and analysis methods available and used at CNI are described on this CNI spectroscopy page.

Additional information (deprecated)

Device specific processing

The General Electric processing includes various steps that can influence the signal-to-noise of your data. We explain what we have learned about this and how to control it in the GE Processing page.

Technical notes

Session Running Script

We advise you to put together a session running script that outlines set up of the scanner and peripherals and positioning of and communications with the participant. You can find an example here (courtesy of Nanna Notthoff, Carstensen Lab).

CNI's Quality Assurance protocol

Weekly QA scans include:

  1. BOLD EPI sequence (analyze mean and variance over time)
  2. DW EPI sequence (analyze eddy current distortion stability)
  3. Spiral field map (analyze long-term B0 stability)

All QA scans are done on the fBIRN agar phantom. The phantom is positioned in the same orientation with the same padding each week. The landmark must be set to the same. The Rx should be not touched (use the same stored Rx). We should do HO shim and set the shim VOI to exactly cover the sphere.

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