September 3, 2010 vNav moco morphometry instructions

Installation Instructions

1. Unzip the file MGH_Moco_Sep_3_10_N4_VB17A_LATEST_20090307.zip onto the C: drive of your Trio's host computer.
2. Inside of C:\Temp\C2P_MGH\ there are four .edx files. The files are named to indicate whether they contain protocols for for 12- or 32-channel coils and whether they are our 1mm isotropic morphometry package or our older anisotropic morphometry package. Import your preferred .edx (or multiple .edx files) at the lowest level of the protocol tree.

Use Instructions

Some very important notes about using the vNav sequences:

1. Please run moco_nav_set for every subject who you want to use motion correction on (we suggest putting it at the top of your protocol with the localizer and autoalign nav). Also, please follow the direction included in the sequence list that says to wait until moco_nav_set has finished making images before dragging the motion-corrected sequences into your scan queue. This is required because moco_nav_set, in addition to making images, saves patient-specific information in files on your scanner's disk every time it is run, and these files need to be written before the moco sequences are put in the patient list and start trying to read them. If you're imaging small children, it's helpful to move the navigator's FOV so that it's not covering their torso as well; for adults we normally just leave it at isocenter and get good results.
2. Please do not try to run the moco sequences while other sequences are still reconstructing their images (i.e., while the little picture icons are grey; when image recon is complete it's a white head on a black background). The moco sequences need to hog the image recon computer and, unfortunately, there's no way for us to request this from the software; we need users to ensure there is nothing else reconstructing while the moco runs. If you try to run the moco sequences while something else is still making images the moco sequence will stop running after a few seconds when it detects that it cannot get data from the recon computer quickly enough. However, you can run other sequences once the moco sequences are done scanning and are just reconstructing images. Since the moco sequences can take a few minutes to reconstruct images once the scan is finished, it's often more efficient to cue up a non-moco sequence after each moco sequence so that you can be usefully scanning while the moco is reconstructing.
3. On the "Special" card of the moco sequences there is an option to "Remeasure # TRs". In addition to the real-time motion-correction, a second part of our system is that you can dial in a number of TRs that you want the system to go back and remeasure for you at the end of your scan. The sequence attempts to detect which TRs were most motion-damaged and then replays them. The cost for this is that it takes extra time. By default we've set this to 0 TRs, so the scans are the same length as before. If you set this to remeasure n TRs, you'll see that scan length goes up by n+1 TRs. Ideally, you'd want to set this so that you reacquire about as much time as you expect the subject to move. In general, we've found that adding an extra 15-30 seconds of scanning to the moco sequences can help correct for situations were someone changes position a couple of times. This may be a parameter you want to play with depending on your subject population.