Operating the Scanner

Scanner Questions

 

      Getting Started

       Interactions with your Experiment

       SMS/Multiband topics

      Operating the Scanner

       Scanner Troubleshooting

What equipment is available?

For detailed information about the quipment available in the CBS, see the facilites and resources page. In addition, there is a resource description located here, under external funding, that can be included in grant applications. For papers, the projector we use is a InFocus IN5542.

How do I join the mailing list?  When is the next safety class?

Everyone using the MRI facility should be on the mailing list, as this is the forum for announcing important information regarding the scanner, where people can announce scan time for trade, or any other information generally of interest to the scanning community.  It is also where upcoming safety classes are announced.  This includes both the full class for new users and the refresher class for current users (required once a year). 

To join the list, go here: http://lists.hcs.harvard.edu/mailman/listinfo/mrusers-list.

What are the general polices and procedures of the scanning facility?

Most of the documentation covered in the required safety training course is located here, including the polices and procedures for scanning.  

How do I schedule time for rooms and/or equipment?

There are several calendars managed via SPINAL that can be found here.  This includes calendars for the scanner, mock scanner, physiology testing room, and behvioral testing room.  In addition, there is information about requesting scan time in general, including how to request recurring time blocks.  Information about how much scan time costs is located here

What funding resources are available?

Information about internal and external funding resources are located here.

How can I sync my experiment with the scanner?

If you connect the usb cable labeled scanner trigger and button box you should receive a ‘trigger’ from the scanner each TR. This comes through as a key press, registering as the ‘=’ sign. You can add a call in your experiment that waits at the beginning until you get the first = sign. Keep in mind in your programming that unless you turn the trigger off once you get the first =, they will continue to be produced throughout the experiment, once for each TR. Some researchers use this to synchronize other aspects of their experiment, while others just ignore them. However, it is possible that a trigger signal could come through at the same time as a button press. In this case, some software packages might only take one of the presses. This is something that you need to test. An alternative is to turn off the trigger once your experiment starts. There is a switch on the box to switch this off. However, I think this might not be the best strategy as it’s easy to forget to turn it off, or to turn it back on for the start of the next run. For more tips on getting triggers and button box responses see here.

How can I get behavioral responses at the scanner?

Similar to the trigger, button box responses come through the usb cable at the scanner as keyboard presses. The right hand button box comes through as 0-thumb, 1-index finger, 2-middle finger, 3-ring finger, 4- pinky. The left hand comes through as 5-thumb, 6-index finger, 7-middle finger, 8-ring finger, 9- pinky. For tips on how to ensure you get responses within Matlab see here.

How do I use the new Celeritas button boxes?

The new button box system uses the large white box on the top shelf above where the old green circuit board is. It has its own USB cable. You will get the trigger and button box responses through this cord, and they have the same mappings as before (The right hand button box comes through as 0-thumb, 1-index finger, 2-middle finger, 3-ring finger, 4- pinky. The left hand comes through as 5-thumb, 6-index finger, 7-middle finger, 8-ring finger, 9- pinky). The trigger is still = (or in matlab +=). The buttons will light up when the subject presses them, and the trigger will show up as a light on the far right labeled trigger. However, the name of the box has changed to Celeritas Dev, see here for how to use this information.

 

Required new step

 

There is one additional step required. The trigger still initially goes through the old green box. This box needs power via the USB cable connected to it. Since you are no longer plugging this into your laptop and giving it power, it needs to get power another way. Please plug it into the black USB plug with the blue light, labeled usb power for green box.

This box provides feedback on the state of the system.

This is what a happy box looks like. Two green lights in the center.

If it is unhappy box , the green lights in the center may be blinking.

Or just one of the green lights may be on.

 

Reset the box

 

To correct any of these issues, hit the reset button on the far right.

 

Suppress the trigger

 

If you want to turn off the trigger after the first one comes through, you can hit the mask button on the far right. A yellow light will appear above the button, and when triggers come through, the trigger light will be yellow instead of green. Please turn the trigger mask off at the end of your session by hitting the mask button again.

 

In the scan room

 

Inside the scan room they are hanging on the wall. The boxes have an attachment to strap the on to the participant's arm. This should prevent them from dropping them. The angle of the box with regard to the wrist strap can be adjusted by loosening the screw on the back and angling it. They wrist strap can also be removed completely by unscrewing the screw in the back. Just make sure to replace it after you scan for the next user.
The cables for these are a little cumbersome, as they made to not be able to bend sharply, and should not be bent or stepped on, as they are fiberoptic and fragile. If they get to tangled, you can separate the cable in the middle (gray connectors) and letting the cable uncoil. If you do this, the box will loose connection with the button box. The green light won't be on next to which ever one you disconnected. To fix this, the box will have to be reset.

Why I am I missing the trigger or the occasional button box response?

Generally speaking, keyboards are not the best way to transmit time critical information to a computer. Keyboard input is typically logged into a hardware buffer, which is lazily queried by software with the full assurance that no key presses will be missed. This is why one has the occasional experience of typing into a document or web browser without seeing a change on the screen until seconds later when a stream of characters appears nearly instantaneously. At such times, the software (or OS) was too busy to interact with the keyboard but all the key presses were faithfully logged into the buffer. There are a multitude of software languages and programming environments that allow users to get information from the keyboard buffer. While we certainly are not aware of the entire spectrum of techniques that users of the MRI facility employ, we will focus on Matlab and the Psychtoolbox to demonstrate a few ways to interact with key presses, and suggested the a preferred method. One of the issues that contribute to some users experiencing missed triggers or button box responses is that the signal coming from the scanner lasts about 8ms. In general, that is very short, and if your computer is busy doing something, they may not register depending on what way you are using to poll the keyboard. In matlab, there are two main strategies for reading keyboard presses. The first, and recommend method, is a kind of buffer, where keyboard presses are stored and then can be read back at anytime. This utilizes a set of function calls based around "KbQueueCheck" which looks into the keyboard buffer for key presses. Unfortunately for some, Docs@Psychtoolbox states that this routine is only for Mac OS X 10.3 or later. Of course, other routines are available for Windows users. Psychtoolbox offers "CharAvail" to query the keyboard buffer and "GetChar" to fetch the character information when its present. Docs@Psychtoolbox suggests that there are problems using this call when implementing Java, but seems to imply that it will work when using Windows -nojvm Matlab. These two approaches should be contrasted to the algorithm that many groups appear to be using. This problematic technique relies on functions based on "KbCheck". "KbCheck" does not query the keyboard buffer for stored characters but rather asks if a key is currently pressed down. KbCheck is placed in a loop that tries to cycle fast enough so that it can poll the keyboard directly without missing a key press. However, given the short (8ms) times that the keys at the scanner appear to be pressed, it is easy to miss them if you are constantly updating your stimulus, or use the KbCheck(-1) to check all devieces, which takes longer, or even if you have the waitsecs(.01) in your checking loop that they suggest to keep from having your priority demoted. For more details see. And for an example, see.

Can I record eye movements during scanning?

Yes! You can, with our Eyelink eye tracker system. To learn how to use the system, please contact Stephanie at smcmains [at] fas [dot] harvard [dot] edu. The system is fairly easy to use, particularly for those who feel comfortable with Matlab. You can communicate with the eye tracker from Matlab, making it easy to convert any pre-existing experiment into an eye tracking experiment. Alternatively, if you are not comfortable with Matlab and prefer more of a GUI oriented experience, Eyelink comes with its own package for designing your experiment and analyzing the data.

How do I calculate degrees of visual angle at the scanner?

To calculate degrees of visual angle, you need to know the viewing distance and size of the projected image. The viewing distance is measured from the screen to the mirror to the subject's eyes. Therefore, it does vary for each person, so this is only approximate. It will be most accurate if you align the laser of the scanner to the marks on the coil, and make sure the participants brow is lined up with the marks on the coil.

Viewing distance: new Prisma: 104cm, old screen location: 95cm

Width of displayed image is approximately: new Prisma size: 41.9cm, old size: 43.5

Then there are several ways you can calculate it, but this is what I have used:

pix_per_deg = pi * rect(3) / atan(mon_width/viewing_dist/2) / 360;

Where pi is the mathematical term, approximately equal to 3.14159 and rect(3) is the size of the screen (in pixels) in the horizontal dimension, or the horizontal resolution. Then, you can specify the size of your stimulus in degrees of visual angle, and multiple it by pix_per_deg to get the number of pixels it should be. For instance if you wanted a square of 5 degrees, the length of a side should be 5*pix_per_deg pixels.

With the new Prisma setup, the eyetracker and regular screen are at the same distances/size. Therefore use the numbers above. For reference, the old information for the eyetracker on the Trio was:

Viewing distance: 107.5cm

Width of displayed image is approximately 41.5cm

In what order does the scanner acquire EPI slices?

If you have multi band/SMS data, please see below. There are three options for slice ordering for EPI. To understand the ordering you first need to know the Siemens reference frame for the slice axis: the negative direction is (Right, Anterior, Foot) and the positive direction is (Left, Posterior, Head). The modes are then:

Ascending - In this mode, slices are acquired from the negative direction to the positive direction (foot to head for axial slices)

Descending - In this mode, slices are acquired from the positive direction to the negative direction (head to foot for axial slices)

Interleaved - In this mode, the order of acquisition depends on the number of slices acquired.   If there is an odd number of slices, say 27, the slices will be collected as:

1 3 5 7 9 11 13 15 17 19 21 23 25 27 2 4 6 8 10 12 14 16 18 20 22 24 26.

If there is an even number of slices (say 28) the slices will be collected as:

2 4 6 8 10 12 14 16 18 20 22 24 26 28 1 3 5 7 9 11 13 15 17 19 21 23 25 27.

Interleaved always goes foot to head, i.e. negative to positive direction.

The slice order is set from the “Series” pull-down menu on the Geometry tab. Do not confuse this with the “Multi-slice-mode” option on the same tab, which would seem to be the more logical name for this parameter – but isn’t.

The time that each slice is acquired within the TR can be found in the DICOM header. Contact Ross at rmair [at] fas [dot] harvard [dot] edu if you need information on this.

How do I use the slice order information in my analysis?

Because the order of slices is dependent upon the scanner type, slice acquisition type, and number of slices, most MRI analysis packages have a place to put this information in. It is most commonly used during slice time correction, which needs to know the order of slices to correct for the difference in acquisition time for each slice.

SPM: In the slice timing module, you need to set the slice order (listed above, which differs for odd/even interleaved slices, and for every protocol if using SMS/multiband ), and you must set the reference slice, or the slice to be corrected to. [see below for information and issues on reference slice selection]


For SMS scans, you must use SPM12, or newer, which allows you to enter a time that each slice was collected. In general, people have then been choosing the reference slice to be the first one, or 0 for time 0.

AFNI: You must set the order of slices regardless of if you plan to do slice time correction or not, within to3d: For interleaved odd: alt+z, interleaved even: alt+z2. Then, if you perform slice time correction, you can set the reference slice within 3dTshift.
For SMS scans, you must read in a text file with the timing for each slice. This should be provided in to3d and 3dTshift, where it might be safest to choose the first slice as the reference.

PROCFAST: A homegrown script from the Buckner lab for preprocessing. This script has hardcoded information about slice order and the reference slice. It assumes the interleaved odd slice order (1,3,5,2,4) for all data, and chooses the middle slice as the reference (using the odd slice order). If you have data with an even number of slices you can either 1) edit the information within fsl_preprocess, the script that does the slice time correction. This can be done by copying fsl_preprocess to your local directory, editing it, and adding it to your path so that it is used. You need to edit line 210 for the slice order (sliceOrder) and 231 for the reference slice (middleSlice). Alternatively, if you just want to change the slice order, you can do this by setting the variable sliceOrder. In bash, type:
export sliceOrder=”2:2:<# of slices> 1:2:<#of slices>
where <# of slices> is replaced by the number of slices you have. You can verify that your changes worked by looking at the output of the script. Shortly after it says ‘Performing slice time correction’, the script launches matlab. Right at the beginning of the matlab call it gives the slice time correction command, you want to make sure the numbers shown in italics below are correct:

Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.

< M A T L A B >
Copyright 1984-2007 The MathWorks, Inc.
Version 7.4.0.287 (R2007a)
January 29, 2007

To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> spm_slice_timing_noui(P,[2:2:12 1:2:12],2 4 6 8 10 12 1 3 5 7 9 11,[3/12 (3 - 3/12) / (12 - 1)]) >>
SPM2: spm_slice_timing_noui (v2.20) 16:15:18 - 11/08/2011 ======================================================================== 
For SMS data, you can not do slice time correction, as this uses an old version of SPM which can't do it correctly. If you would like to bypass slice time correction, please send an email to Stephanie (smcmains [at] fas [dot] harvard [dot] edu) who has a work around for skipping slice time correction.

Note on Reference Slice:

Often, people use the middle slice as the reference slice with the reasoning that the most any slice will be corrected by is ½ a TR. However, this has implications for the timing of your stimuli, as you just essentially shifted your 0 point by half a TR. To correct for this, your stimulus onset times need to be shifted back by half a TR (i.e. times = times-1/2TR). Alternatively, for simplicity, some people correct to the first slice, this eliminates the need for any correction of your stimulus onset times. There is some controversy about whether SPM can correctly read the slice order/reference slice information when performing a FIR analysis to extract time course information (reported 11/2011). This seems particularly an issue when taking the output from procfast. Therefore, it is recommended to use the first slice as the reference in this case.

Should I use interleaved slices?

For EPI-BOLD scans, the majority of users currently tend to use interleaved slices; for instance, all odd slices followed by all even slices: 1,3,5,7,…2,4,6… By interleaving, a time of TR/2 is left between the excitation of any one slice and either of its next-nearest neighbors, thereby minimizing crosstalk (partial saturation) between them and maximizing SNR.

Historically, interleaving was used to overcome the imperfect RF profile of the excitation RF pulse. In an ideal world the frequency profile – and hence the spatial profile of the excitation (or slice selection) pulse - would be a perfect square. In reality, however, excitation RF profiles tend to be more trapezoid-like. The first consequence of non-square slice profiles is one of nomenclature. When we talk about slice thickness and slice-to-slice distances we need to define the point on the profile we’re using as our reference. The standard convention is to take the half-height width as the slice width, and define inter-slice distances accordingly. This is not a universal rule, however, and empirical testing by those at UC Berkeley suggests that Siemens uses something like 5% or 1% above baseline to define its slice thickness. (In other words, when you ask for a 3 mm slice the base of the trapezoid would be 3 mm but the half-height might be only 2.95 mm.) Now let’s look at the inter-slice overlap issue from a practical standpoint, and address the issue of interleaving. The Berkeley study revealed that with sequential slices, the slice SNR remained at its maximum (100%) level when using gaps of 5-20%. Only when the gap was reduced to a nominal 0% gap was there a very slight decrease of image SNR, to 99%. (This is how we estimate the Siemens convention of using the base of the trapezoid to define slice width.)

These results have two consequences. Firstly, it means that you can use gaps of 5-20% without getting appreciable saturation effects, and even no slice gap has minimal effects. Secondly, the implication is that interleaving isn’t necessary to mitigate slice crosstalk; the slice profile takes care of most of it.

Now that we have seen there is no strict reason, other than historical precedent, to use interleaving, what are the differences between interleaved and sequential slicing? Does one provide a definite advantage over the other? In the absence of head motion the answer is ambiguous: there is almost no difference in performance. But whenever the subject moves his head in the slice dimension (through slice movement) the consequences for interleaved slices can be more severe than for sequential slices. In the case of sequential slices, the movement would cause some new anatomical regions to be included at one end of the slice stack, while some other anatomical regions disappear from the other end; i.e. the brain moves through the slices. The same motion would cause a slice-to-slice signal intensity variation when using interleaving, but only for the duration of the movement. That is because as the movement occurs we are going “up and back through” with the slices, rather than slicing in a single direction, as with sequential slices. In effect, it is as if we have changed the effective TR for the slices.

So what is the best approach? The most robust approach seems to be using sequential slices acquired head-to-foot, or in descending order. Sequential slicing will avoid the striping that might happen because of certain types of head motion, while going “top to bottom” with the slices will minimize interference from the inflowing blood (ASL-like) enhancement of functional contrast. This is what is currently recommended by the SPM group and by the SPM course affiliated with the Martinos center.

Can I view dicoms on my computer similar to on the console -> or my dicom conversion went wrong, how can I verify its my conversion script and not my data?

Yes – and we strongly encourage it! This should be your first step for checking you have all the images you think you have, and that they look how you expect them to look, when you run into problems converting the DICOM’s to nifti/analyze/other formats for offline processing.

All users should download a DICOM viewer for their offline computer. This a powerful yet very simple software package that will let you see all the DICOM images you may have archived to a DVD, or exported to a FLASH or portable hard drive. And they’re free! These packages will read all the information from the DICOM header and arrange each of your scans in order, allowing you to view all slices or time-points just like you can on the scanner, no matter how arcane, obscure or verbose the file-naming convention was when the files were exported.

If you are using a Windows PC, we recommend Syngo FastView, from Siemens. It may not be the best DICOM viewer, but its interface is very similar to that on the scanner, so might be the easiest for a newcomer to navigate. Syngo FastView is downloadable from here (Click “Confirm and Continue” if prompted when the page appears – do NOT click “go to our US site”). If you are using a Macintiosh, we recommend use to recommend Horos, which will import your Osirix database (our old recommendation) if you had one. It is available from here. For Linux, we recommend MRIcron. This package is available on the NCF, so if your data is archived there via CBS Central, it can be checked with MRIcron if need be without moving the data further. MRIcron also has versions for Windows and MacOS, if you want cross platform compatibility. MRIcron can be downloaded from here.

In what order does the scanner acquire EPI slices for SMS/multiband scans?

If you’re doing any form of slice-time correction with your data, you need to be dealing with the fact that multiple slices are now acquired at the same time and conventional slice time correction algorithms wont work. (This is not new to the Prisma – but has been the case for the last 18 months!)


What is new is that the slice-time information is now accurately detailed in the DICOM header of your SMS_BOLD images. The information is in DICOM field 0019,1029. This is part of the Siemens dedicated section of the header – some command line tools that are part of, eg. Freesurfer or AFNI may not show the information. But DICOM viewer programs like Horos version(Mac) or Syngo FastView (Windows) will show this information in the tabulated view of the DICOM header. Unfortunately, DicomBrowser on the workstations doesn't show the information, so you will need to transfer one of the dicoms from a run to your local machine by following these instructions.


For the three most common protocols, I have put timing files on the ncf. You can copy them from: /ncf/mri/01/users/shared/times_for_sms.

How do I convert my new SMS images correctly?

The only reason there is any difference in this regard, is that the numbers coming out of the SMS-BOLD scans are larger, which can be a problem for some conversion problems if they aren't reading the bit format correctly.
It used to be (and for Siemens sequences, still is) 0-4095. For the SMS-BOLD sequence from Minnesota (and all Siemens sequences after the next upgrade next year) the intensity range is 0-65535. This was done because as high-array head coils (32ch, 64ch) have come to predominate, the range of intensities across the head has become much larger than it used to be in the days of the 12ch (or 4ch, or 1ch!!) coils. To avoid getting trivially low numbers in the middle of the brain, everything has been scaled up.


The DICOM conversions seem to fail for voxel intensities above 32768 - anything above that gets converted a large negative number, which can look like black voxels where there should be bright white ones. This usually happens at the top of the head where the numbers are largest. If you have image series where no voxels have values above 32768, then the old routines will still work.


There are various solutions based on your analysis program.
SPM: avoids converting, so you don't have to worry - unless you like to take the output from SPM and input it into another program, then you should verify the conversion happens correctly.


mri_convert/Freesurfer: This is part of freesurfer, and also used by fc-fast. Doug (from MGH) was nice enough to correct this for us, and Tim (your local NRG member) made a module for it. So please source the module below, it MUST be sourced after you source your freesurfer version. For instance, if you want to run fc-fast, you should source the following, with the last line being the critical module for the fixed mri_convert, the first two being critical to get the new module system and the ncf modules.
source new-modules.sh
module load ncf
module load freesurfer/5.3.0-ncf
module load mri_convert/2015_11_09-ncf


AFNI: in to3d you need to include the –ushort2float flag. This is only available in the newer versions of AFNI (available via list_loaders or through modules). So make sure you are loading a more recent version than the default.


dcm2nii: Also only works in the more recent version (2012_12 via list loaders)

How do I acknowledge the creators of these new protocols and the new scanner?

The new scanner was paid for in part from a NIH grant to the center, and it should be acknowledged when presenting or publishing data collected on the Prisma: NIH grant S10OD020039, along with the general support received from the Center for Brain Science

The SMS-BOLD sequence we are using was developed at the Center for Magnetic Resonance Research (CMRR) at University of Minnesota. It is not part of the Siemens product line of sequences, nor a Siemens development (Works-in-Progress) package. Under agreements with Siemens, CMRR is allowed to distribute versions of their sequence to other sites, but are not allowed to charge money for it. As such, it’s a free scientific collaborative exchange, and the terms of the agreement specify that we must acknowledge CMRR and cite their prior publications when any work employing their sequences is written up/reported. When writing up or reporting your work in any format (manuscript, abstract, presentation), please acknowledge the receipt of the software from the University of Minnesota Center for Magnetic Resonance Research in the acknowledgments section. In all manuscripts, abstracts and presentations the following papers should be cited:


Moeller S, Yacoub E, Olman CA, Auerbach E, Strupp J, Harel N, Ugurbil K. Multiband multislice GE-EPI at 7 tesla, with 16-fold acceleration using partial parallel imaging with application to high spatial and temporal whole-brain fMRI. Magn. Reson. Med. 63:1144-1153 (2010).
Feinberg DA, Moeller S, Smith SM, Auerbach E, Ramanna S, Glasser MF, Miller KL, Ugurbil K, Yacoub E. Multiplexed Echo Planar Imaging for Sub-Second Whole Brain FMRI and Fast Diffusion Imaging. PLoS One 5:e15710 (2010).
Xu, J., S. Moeller, E. J. Auerbach, J. Strupp, S. M. Smith, D. A. Feinberg, E. Yacoub and K. Ugurbil. Evaluation of slice accelerations using multiband echo planar imaging at 3 T. Neuroimage 83: 991-1001 (2013).


Failure to acknowledge could result in our Center losing the ability to receive other new advanced methods under development at CMRR in the future.


Please note: this acknowledgement is different from the one that should be used when reporting studies that employed the SMS-BOLD technique on the Trio scanner. Contact Ross (rmair [at] fas [dot] harvard [dot] edu) if you are reporting work completed on the Trio, and need the appropriate acknowledgements.

What is the SBRef image? Or why does each scan show up as two in CBSCentral?

You should notice a single time-point image with “_SBRef” appended to the series name, for each one of your SMS-BOLD scans: This “Single-Band Reference” image is what the scanner is acquiring during the 10-20 seconds of reference scans before the first trigger is sent, and your first real time-points are acquired. This image matches your real brain-volumes, but is just acquired without slice acceleration. The scanner is acquiring it anyway, so why not have it stored with your data?

The WashU/UMn HCP consortium recommend using this SBRef image as the starting point for motion correction, and for alignment of your BOLD images to anatomical images. Especially if you’re using a short TR, the SBRef image will have superior SNR and contrast to your BOLD scans, which is why this method is suggested.


See: Glasser et al, The minimal preprocessing pipelines for the Human Connectome Project, NeuroImage 80 105–124 (2013).

What kind of scanner do we have?

The CBS Neuroimaging Center operates a 3.0 T Siemens Prisma whole-body MRI system (Siemens Medical Solutions, Erlangen, Germany) which is fully equipped for advanced brain imaging. More information on the scanner can be found here.

How do I register a subject on the scanner?

There are four task cards along the right hand side of the screen: EXAM, VIEWING, FILMING, and 3D (red arrows, below).

EXAM is the interface that allows us to acquire data.

VIEWING is where you can look at images that have been previously collected.

FILMING is where you can prepare images to be printed (see below).

3D allows you to view 3D datasets (Structural MPRAGE) in all three orientations.

You want to select the EXAM card to start your study.

Next, in the Patient pull down menu (top left hand corner) select Registration. Alternatively, press the key on the keyboard (right hand corner) that has a small man and a keyboard on it.

Pressing this will also bring up the registration. A form will appear and you need to fill in all the boxes that have bold writing (black arrows, above). You will not have an option to click EXAM until all these are filled out. Remember never use patient identifiers as this is a violation of the Health Insurance Portability and Accountability Act (HIPAA).

The proper naming convention is YearMoDay_XXXX, where X is individual lab’s preferred coding convention. (example: 120124_subj1_exp1 for January 24 2012).

This should be copied and pasted into the Patient ID field.

Date of birth should be listed with the date and month as 1, and the actual subject’s year of birth (example: 1/1/1980)

Do not forget to select the sex, this is often missed.

Enter the subject’s weight in pounds.

For the study, press the arrow and click on INVESTIGATORS, then select your name or the name of the PI.

If you will be sending your data to CBSCentral, and want to skip limbo and have your data go directly to the correct project, you can add a field to the Study Comments box via these directions.

For patient position press the arrow and select the first option. Head First - Supine. This is very important.  If you acciedentially select the second one, your slices will be reversed, instead of going from the bottom to the top of the head they will go top to bottom.  Watch out for this as it is easy to do.  The easiest way to correct this if it happens is to reregister the person and start over.

Although they are not mandatory for scanning you should enter the PI’s name in the physician box and your name or initials in the operator’s box.

When the information is entered press the exam button. Another window will appear asking you to verify that your information is correct. If it is, press confirm.

 How do I conduct a typical scan?

For a summary of our default protocol see here. On the lower right half of the screen all of the sequences within the protocol you selected during registration will appear. To actually scan you must move them over to the lower left by dragging them over (Fig. 1, arrow), or highlighting the sequences you want and click the (<<) button.

Figure 1

The first sequence is always a localizer. If you look on the right of the localizer sequence you will notice that the localizer does not have the small “working man” icon beside it, as the other sequences below it do, shown in Fig. 2 below (red arrow). The lack of this icon means that as soon as the localizer is moved to the left side it will automatically run. Make sure you let your subject know! All of the parameters have been pre-programmed.  As soon as the localizer is complete, the single-slice sagittal, coronal and axial views will fill the viewing windows at the top of the screen.

Figure 2

2. Second is often Autoalign, which allows the slice placement of subsequent scans to automatically align (For BOLD scans, the default slice angle is parallel to the AC/PC Line). In Fig. 2 above, AutoAlign is running, while the MEMPRAGE protocol is “open” because of the working man icon. The yellow boxes show the default position of the field-of-view for the MEMPRAGE scan, based on the position and orientation parameters on the right (red box). When Autoalign is acquired successfully an icon with a yellow line appears (Fig. 3 below, red arrow), if it was not successful it appears with a red line. When AA Scout completes, it updates the field-of-view position based on the subject’s head position – note the yellow boxes have moved, and position parameters have changed. If you have not yet put the MEMPRAGE or any other protocols in the scan queue, when you move the next sequence to the scan queue and open it, (by either double clicking on it, hitting the open button, or right clicking it and selecting open), it will open with the field of view properly positioned on the brain based on the AAScout results (i.e. tilts slice box to compensate for the subjects positioning). However, if you do not use the Autoalign, or don’t like the way it aligned your slices, you are responsible for positioning the slice prescription for the rest of the protocol (see below). Also, please note that Autoalign uses the body-coil, so if you happen to notice this, don’t worry, it is correct.

Figure 3

3. If it’s not already there, the structural scan (T1 MPRAGE or MEMPRAGE) should be brought to the left panel and opened as described above. Once opened, the sequence parameters will be in the lower right side panel. The parameters are displayed on many tabs but always open on the Routine Card (Fig. 3, above). Check the position of the yellow field-of-view/slice box. Anatomy cut off (such as the nose) can wrap and end up in the occipital lobe, so make sure you try and capture the nose within the box. If needed, you can move or tilt the slices (volume). Left clicking the center dot (in the middle of the yellow box, with the double lines going through it) allows you to move the volume. If you need to rotate the volume move the cursor over the centerline until you see a circular double arrow, hold the left mouse button down and rotate as needed. Grabbing any of the sides can change the FOV or slice thickness (not something you usually want to do). Tell the subject that the sequence is going to begin and click “Apply”.

 

                                Figure 4a                                                                               Figure 4b

4. Wait for the MEMPRAGE reconstruction to finish. This may take a few seconds, especially if the 32-channel coil is used. When the head icon (Fig 4a) is hollow, the reconstruction is still going on. When the reconstruction has completed, a head profile icon will now be solid (Fig. 4a). Click on this icon. If only one series is present, drag the icon with the left mouse into one of the three window segments (Fig. 4b). If more than one series is present under the head profile icon – as will happen if you ran a MEMPRAGE, click on and drag only the highest series number – this is the summed average result of the multi-echo MPRAGE acquisition (red arrow, Fig 4b). Please note that the center slice of this series will appear in the window. Use the dog-ears in the right upper corner to go forward and back in the image series until you find the region you want to view the positioning of your BOLD your slices on. Also, go through the entire series to check for motion.

Next, bring over your EPI run. If AA Scout was used, open the sequence and make sure the automatically centered slices are positioned correctly, then click “Apply”. Please note that on occasion AutoAlign may not position the slices as you desire them, therefore you will need to manually set your slice prescription, as described below. Fig. 5 below shows the slice box for the EPI positioned on the MEMPRAGE image (note the left most image is different from the localizers above).

Figure 5

The actual position of the individual slices can be visualized by toggling the slice view buttons in the slice position toolbar shown at right below. This is found by clicking on the head icon with the purple slice marks (red arrow at right). The individual slices are shown in Fig. 6.

Figure 6

6. The working man icon (red arrow, Fig. 6 above) indicates the EPI protocol is open for editing. If AutoAlign wasn’t used, then you will have to move your slices on your own, covering whatever parts of the brain you are interested in. To ensure you are capturing everything that you want, it is recommended that you run a test EPI functional run with 2 measurements (time points) to ensure the slice positioning and quality are good. You can use your regular fMRI sequence and just change the number of time points manually. This can be changed on the BOLD Card (Fig. 7, arrow), in the field Measurements. Enter 2 and then hit return. This should be done before you run any other optional scans such as the field map or T1w EPI scan. Importantly, you will have to copy the slice placement information to scans coming afterwards, as described next.

Figure 7

If you have other scans, such as a T1w EPI or fieldmap scan to run before the ‘real’ EPIs, you can bring them over. If AutoAlign was used and you didn’t move the slices, then you can just Apply these. If not, you need to copy the slice information from the test EPI. To achieve this, open the sequence and then right click the 2-measurement functional run with the proper slice positioning and select copy parameters from the menu. From the list of parameters you want the second option, slices & sat parameters. For more complete instructions, see here . Now the new sequence slices are in the same location as the 2-measurement functional run. Hit “Apply” when positioned properly.

Bring over the functional EPI and open it. If AutoAlign was not used, or you moved the position of the slices after AutoAlign, copy the slice prescription of the 2-measurement functional run just as you did above. The acquisition time of the scan will be indicated at the upper left corner of the sequence. Remember that the time includes any dummy scans so; deduct number-of-dummies x TR from the time of the scan to calculate the length of your paradigm. Please note, if you are using iPAT there will be additional time added on also, however the first trigger will always come with the first ‘real’ scan. Click “Apply” or “Scan”. For the difference between these two options, see here.

The EPI scans always have a two-step process to begin. Clicking apply begins the pre-scan routine of frequency and shim check. All other scans begin automatically at this point, however for a BOLD scan, you may want to not start the scan until your subject and stimulus computer are ready. The “flag-man” icon (red box, Fig. 8 below) achieves this - instead of the scan starting automatically, a pop up window will appear.

Figure 8

When you have everything ready to go, click continue. The scan begins immediately. If you want more runs with the exact same parameters, right click on the one you want to copy and select append. If you want the same slice prescription but a different # of measurements, right click on the functional, select append, open, and make the changes as described above and click “Apply”.

Make sure to open the Inline Display (Fig. 9, arrows), if it does not open automatically. You open it by clicking the head icon at far right, and can expand it by dragging the corner. Inline Display shows your functional images immediately after the images are reconstructed – image number is given in the upper left of this window. This allows you to monitor if your subject is moving, or if there are unwanted artifacts.

Figure 9

How do I move my slices after autoalign fails?

To move your slices, your cursor to the center of the yellow FOV box. The cursor will change shape, meaning it is safe to drag the box around. If you want to rotate your slices, move your cursor to the edge of the box till you get a double arrow image, then you can drag and rotate. If you drag or grab anywhere else, you could change the FOV, which is bad and can change things like your voxel size.

Once you verify that this is where you want your slices, usually via a test epi of a couple of timepoints (See here for more detail), you will have to copy the slice information to future scans that should use the same FOV, such as other BOLDs, T1w EPI, or fieldmap. To do this, bring over your next scan from the protocol list at the right. Double click it to open it. Then right click the test epi or functional run with the proper slice positioning and select copy parameters from the menu. From the list of parameters you want the second option, slices & sat parameters, then click OK. Now the new sequence slices are in the same location as the 2-measurement functional run. You can hit “Apply” to use the updated slices. This has to be done for every new BOLD run you bring over from the protocol browser on the right. Alternatively, you you are running a bunch of the same BOLDs in a row, you can right click on the current one and hit append, this will place another copy of the run in the list, and will include the updated slice information.

How do I print the slice prescription?

There are two options for this. One is a general method for printing things you want from the scanner and involves grabbing the entire screen. The second way is more specific to printing the slices and uses the print tools within the scanner software.

Printing via Print Screen:

1: Hit the "PrtScr" button at the top of the keyboard, above the cursor keys. A copy of the entire screen is saved on the clipboard in Windows XP.

2: Hit Control and Escape together, to bring up the Windows start-up menu from the bottom left of the screen. Move the Cursor up and choose "Paint".

3: Paint is a crude image processing application in Windows (like Notepad is to MS Word!) You'll get a blank canvas. Use Ctl-V or pull down edit/paste to paste your screenshot into Paint.

4: You can trim the screenshot down to just the desired portion of the screen, if you choose. However - this is done by selecting the sections to delete, so it can become tedious.

5: You can print directly to the printer in the computer room adjacent to the scanner room, although if you print the entire screenshot without trimming, it will print on multiple pages.

6: You can save the screen-shot to your USB FLASH or external USB hard-drive, in jpg, tiff or png format, for later use such as annotating or for inclusion in documents, etc.

Printing within Syngo:

1. Make the sagittal with the slice prescription the active window by clicking on it. A blue box will appear around it.

2. Hit the button in the lower right hand corner of the keyboard that looks like a sheet of film. This will send the active image to the filming page.

3. Go to the filming page, a tab on the right of the screen. The image will be in the upper left hand corner of the page.

4. Go to the camera tab and make sure that the setting is for the laser printer, not PDF. Next, select the layouts, 1x1 option (red arrows above).

5. Click the left icon that looks like a printer with a sheet of film coming out of it (red arrow below), this is the printer. The image will be printed on the printer in the computer cluster room in the basement.  If you want multiple copies, change the number of copies.

How do I print my scan protocol?

Go to the little pencil on the right hand side of the screen in the exam card.

This brings up the protocol tree. Find the correct investigator folder on the left and the correct protocol. Either right click on entire protocol if you want every sequence or right click on the individual sequence you want. Choose print or export depending on if you want to print or save to a memory stick. Choose the correct printer or usb drive and click ok.

How do I send my data to CBSCentral?

Highlight your study in the subject/data browser. The browser can be activated through the patient pull down menu or by hitting the button in the lower right hand corner that has a folder tree file on it.

Highlight your subject or session, but ensure a specific series/scan is not highlighted (otherwise only the highlighted scan will be sent).

Under the transfer menu, select select "send to CBSCentral". Your study will now go to the server.

Once there, you need to archive it according to the instructions here (unless you set the session up to auto-archive when you registered the subject). Otherwise you will not be able to access the data for analysis - but others will be able to claim or delete it! Go back to the transfer menu at the top of the screen and select network job status (see below) to make sure the DICOM transfer is working.

 

You can also look for the network-send icon at the bottom of the screen (below).

 How do I export my data to an external drive?

To maintain your own personal back-ups of your data, we highly recommend the use of a portable USB hard-drive. These are the fastest way to export your data after the network send. In a pinch, a FLASH drive can be used, but these are usually slower, and not recommended for long-term storage.  Make sure what ever storage device choose to use does not want to install any software on the console because you will not be allowed to and then the console computer will not be able to mount the drive. Ensure your USB drive is plugged into one of the USB ports on the front of the scanner computer or satellite console computer. Highlight your study in the subject/data browser. As shown above, highlight your subject or session, but ensure a specific series/scan is not highlighted. Then, use the transfer pull down menu and choose “Export to Offline”.

A second window will now appear. Choose the destination for your exported files. Do not choose a location on the C: drive – this space is needed for the scanner to operate smoothly and data found here will be deleted. USB portable hard-drives and FLASH drives plugged in to the USB port on the front of the computer usually appear as drive F: or G:. Choose the drive where your USB external drive is located, and then click “OK”

Go back to the transfer menu and select local job status (right above network status, as shown above) to make sure the file export is working. You can also look for the data-export icon at the bottom of the screen (below).

How do I make a DVD of my data?

If you need to make a DVD of your data, it is a good idea to do so on the satellite console rather than the main scanner console, as this process takes a long time and may interrupt those scanning after you.

1. Label a DVD and put it in the second drawer of the satellite console computer labeled “DVD Burner”. Make sure you do not hit the round silver button. This shuts off the computer, it does not open the DVD-R. There is a small black button below the drawer that opens it.

2. Go back to the browser and ensure your subject/session (but not individual series/scans) are still highlighted (as shown here). Go to the transfer pull down menu and select “Export to”.

A second window opens in which the DVD-R is the only option. Click export.

If doing this on the main console, from the transfer pull-down menu, select archive to DVD-Burner.

3. Next, a window appears asking you to label the DVD. There is also a check box that you can click if you want the Siemens Syngo FastView DICOM viewer on the DVD. Enter a title for your DVD, and add the viewer tool if you want to be able to look at the DICOM images on a remote Windows PC. (This will allow you to check the DICOMs appear on the DVD as you expect.) Then click OK.

4. Go back to the transfer menu and select local job status (right above network status, as shown above) to make sure the DVD transfer is working. You can also look for the data-export icon at the bottom of the screen (below, left).

 

Once the data has been exported, a DVD icon (a DVD with a red ball on it) will appear on the bottom of the screen, indicating the DVD is burning (above, right). When the icon is gone, the burning is complete. To ensure compatibility with other DVD drives, the DVD should now be “finalized”. Again from the transfer pull-down menu, choose “finalize medium and eject from DVD-Burner”.

The disk will be finalized, and then ejected when this is complete. This message is also seen at the bottom of the screen:

If that data does not fit on one DVD a pop up message will appear when the first DVD is finished. You should click eject, and insert a blank DVD. You then must click retry to continue burning your exam (retry burns the second disk, it does not retry the first DVD!)

Why does the scanner instruct me that the patient bed might move when I start the first scan in my session (usually a localizer)?

Until a reference scan has been acquired, the scanner is using as its frame of reference the magnet isocenter - the center of the magnetic field, which is in the geometric center of the bore tube. This could, in principle, differ from the reference position, called REFERENCE, which we use. The reference we want to use is the center of our subject’s head, which we have just marked with the laser prior to putting the bed into the magnet. As soon as a localizer (or any other image) has been acquired using the REFERENCE positioning mode, the scanner software then ‘knows’ to reference all subsequent images relative to that first image. This allows you to prescribe slices on each subsequent image however you like, and the scanner will track where you are in space. This stays true throughout your scan session provided you don’t move the patient table.

I want to know how long my scan will take. Where is the scan time shown?

On the Exam display, look approximately halfway down the screen, below the three image display windows and immediately above the parameter card area. In a violet/blue color is a line of information, for example:

The information above is interpreted as follows:
- TA - time of acquisition, 6 mins 12 seconds. This includes time for dummy scans and any additional reference scans needed if using iPAT.
- PM – parallel mode. REF indicates reference positioning mode, meaning the slice position is set relative to the patients head or the auto-align information.
- PAT Off indicates iPAT (parallel imaging) is not in use for this scan. (When parallel imaging is turned on with an acceleration factor of 2, this reads PAT: 2)
- Voxel size is 3.0 x 3.0 x 3.0 mm. To get voxel size with two decimal place precision, place the mouse over the Voxel size field. It pops up in a new text box, as shown above.
-  Relative SNR you can ignore. It will always appear as 1 unless you change acquisition parameters.
- epfid: The abbreviated pulse sequence family being used is labeled as epfid. Place the cursor over the epfid word and a popup (below) will tell you which exact pulse sequence (binary file) is in use – in this case, “ep2d_bold_MGH”.

What is the difference between the Scan and Apply buttons for starting a scan?

Somewhat counter-intuitively, the Apply button initiates the acquisition for the current scan and doesn’t alter anything else in the scan queue. The Scan button also initiates the current acquisition, but it also makes a clone of the protocol and appends (or inserts) it immediately after the scan that has just been initiated. So the Scan button could be used for a series of identical EPI acquisitions, say, without the need to bring over a fresh protocol or use the Append menu item to make a protocol clone. As far as the acquisitions themselves are concerned, however, there is no difference.

I want 200 volumes in my EPI time series. How do I do that?

On the Exam task card (the main environment where you drive the scanner), select the BOLD tab on the parameter window. The number of volumes is specified by the rather cryptic parameter called Measurements. Just enter 200 and hit the return key. You will get 200 volumes of EPI data stored on disk, and you’ll get 200 trigger pulses from the scanner to control your stimulus script. You’ll get 200 trigger pulses no matter how many dummy scans there are, and regardless of any reference scans for iPAT. In other words, dummy scans and reference scans for iPAT don’t emit trigger pulses.

How much subject movement is too much?

This is very subjective! At the end of the day, only the results of a full analysis can determine whether your subject(s) moved too much. As a rough rule of thumb, though, users report that rigid body realignment numbers of less than 2 mm of movement in any one axis over the duration of a time series (say 200 EPI volumes) is normally acceptable for getting activations that make sense, and without too many false positives. The more you scan and the more data you analyze, the more likely you are to be able to tighten this criterion and perhaps add your own empirical assessment that you can use during a scan session (where you have a chance to fix the problem). Most often this means watching the Inline Display closely for glaring examples of subject motion (yawning, nose scratching, head movement coincident with respiration because you didn’t pack the head very well, etc.)

You can also quickly check for significant movement during a BOLD scan as soon as it has ended, while the subject is still in the magnet. The scanner allows you to calculate a time-series standard-deviation image from your time-series BOLD scan.

Areas where signal intensity has changed a lot during the time-course appear bright, while other areas appear dark. The eyes are usually bright, however a bright ring around the head (red arrows on the left standard-deviation map) might indicate significant motion (right image shows a separate run with less motion).

You can also simply load a BOLD run into the viewer and scroll through the images. This will give you a sense of how much movement occurred and over how many timepoints. Ideally, one of these methods would be performed at the end of each run so that if there is a lot of movement you can give the subject feedback and/or you can re-collect that run of your experiment (if your experimental paradigm allows you to do this).

I can’t hear anything happening? How can I tell what the scanner is doing right now?

 

Look in the very bottom left-hand corner of the screen. It might say, for example: “Waiting for scan instructions,” or “Waiting for slice positioning,” or “Scanning 00:36 (3/20 B).” That last message tells you there are 36 seconds left in the current scan, and that it’s just finished acquiring three of twenty blocks in a time series. The other messages are usually self-explanatory.

How do I reset the table?

If the table freezes or you accidentally hit the table stop button on the intercom, there are two quick solutions. Hit the red 'stop' button on the side of the scanner and then hit the table in/out buttons back and forth until you hear a "click". Then press the table forward once and release. Watch for an arrow to appear at the head and feet of the icon on the display. The table is now reset.  Alternatively, you can hit the host standby button on the gray siemens box in the control room.  Wait a minute, and hit the on button.  Wait for 3 beeps from the scanner and the table should be reset.

The scanner doesn’t seem to be working properly, how can I tell what is wrong and what can I do?

All warnings and errors are represented as pop up boxes and/or as icons at the bottom of the screen. This is what it looks like without any errors:

The green pie chart indicates how full the system’s image storage capacity is. Holding the mouse over the pie chart gives the exact database capacity in a pop-up. We keep this under 70% to ensure smooth operation of the scanner. The waveform indicates the scanner’s acquisition system. When there is a warning about a particular system, there will be a yellow line through it:

When there is an error, there will be a red line:

To view what the error/warning is, click on the icon. A pop up box will have the message. If you choose okay, it will clear the message, so it is generally better to press the close button so that these don’t get cleared. It is also a good idea to write down or take a screen shot of the message so that you can relay it to Ross (rmair [at] fas [dot] harvard [dot] edu) and Tammy (tmoran [at] fas [dot] harvard [dot] edu). This is true for messages that start as a pop up box also. If you have an error/warning during regular business hours you should try and contact Tammy, Stephanie, or Ross (in that order) for help on how to solve the problem. Their contact numbers are listed on the white board in the scan room. If it is after hours you can try Tammy’s cell phone. If she doesn’t pick up you can leave a message and she will get back to you if she can. However, there is no guarantee; that is the risk that comes from scanning outside of business hours. There should usually be someone around from 9-5:30 during weekdays. If you can’t get ahold of anyone and feel brave enough (aka experienced enough) to troubleshoot on your own you can try some of the tricks below. After noting the error/warning you can check on the status of that component via the System Manager. To access this, go to System (located in the bar at the top of the screen), and then go to Control via the pull down window.

This will bring up a box with four tabs at the top - host, image recon system, MR scanner, and tools (see below). You can check the tab that corresponds to the error message, or when in doubt, look at them all. If things are working, they will have green checks and Xs. If any of them is red, that means there is a problem (or the application is not running). The first thing to try is just rebooting the part that has the error.

If the error is on the host tab, you can choose from several options (see above):

1. Restart an individual application (Exam, Viewer, Filming, 3D, etc…). Click on the appropriate application, and then click restart application – top right arrow above. (Time to complete about 30 seconds)

2. Restart the Siemens Syngo program. Click “Restart syngo MR” (Time to complete about 5 min).

3. Reboot the Host computer. Click the “Reboot” button. (Time to complete about 10 min).

4. Restart the entire system. Click the “shutdown all” to shutdown the entire MR scanner system. Once the screen states it is safe to shutdown you will need to press the blue “system off” button on the Siemens Alarm Box. Wait for a couple of minutes and the press the blue “system on” button. (Time to complete about 23 min).

Also note that some error messages are likely to appear during the host computer shutdown and start-up - you can click through these as the appear, and do not need to be reported. Also, on startup, you'll see some brief flashes of a windows desktop, and there is a point where the system looks like it has stalled. When you see a completely black screen with just the mouse cursor arrow, you need to hit the spacebar to continue.

If the problem is on the Image Reconstruction System tab (see above), you can restart the image calculation software (time to complete – about 30 seconds). If this doesn’t solve the problem, reboot the image reconstruction system by clicking the reboot button (Time to complete about 3 min).

If the problem is on the MR Scanner tab (See above) you have several options:

1. Reboot the operating system of the MR scanner by clicking the “Reboot” button (Time to complete about 3 min).

2. Switch the scanner to Standby, which basically shuts down everything but the console, by clicking the “Stand By” button. Once it says the scanner is in standby mode, you need to bring it back online by clicking the “System On” button on the MR scanner tab (Time to completion about 5 min).

NOTE: Whenever anything has happened that requires a reboot of the host computer or a shutdown of the scanner, please return to the System Manager after everything comes back online. Go to Systems (top of the screen)-> Control and then select the Tools tab (see above), and click “Save System Log Files”. This creates a very large file of everything the scanner was doing. Siemens accesses this remotely, and can diagnose what caused the problem. This takes about 20 minutes, but runs in the background. A pop-up window will appear when the SaveLog is done.