tag:blogger.com,1999:blog-4402160631955197288.post2214415378314240687..comments2024-03-12T19:57:17.818-07:00Comments on practiCal fMRI: the nuts & bolts: Shim and gradient heating effects in fMRI experimentspractiCal fMRIhttp://www.blogger.com/profile/07387300671699742416noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-4402160631955197288.post-15478736143353605882014-10-19T21:07:01.324-07:002014-10-19T21:07:01.324-07:00Hi Daniel,
So there are a few things going on...Hi Daniel,<br /><br /> So there are a few things going on that cause MCFLIRT, or any other realignment method, to find "motion" in a time series acquired from a stationary phantom. First, although there's no time axis in MCFLIRT, you're presumably applying it to a time series of EPIs and the output plots represent that same time series. These plots represent the (in)stability in the images from frame to frame (i.e. from TR to TR).<br /><br /> There are significant drifts in thermal properties of the scanner gradients with time (i.e. with ongoing use) that manifest primarily as shifts in the phase encoding axis, i.e. as in-plane translations. However, the realignment algorithm may interpret other instabilities, too, e.g. changes in the center of mass of the signal from thermal instability in the RF amplifier (which on many older scanners is air-cooled). It doesn't differentiate between these different changes, it simply applies its cost function and returns the best fit. We might consider these "systematic shifts" because their underlying properties are real, physical effects that can be reduced with better hardware. Then there is the sampling issue. The typical voxel size is 3 mm on a side. Now check the size of the motion parameters being returned by MCFLIRT. Very much less than a mm! How can that be? It's sampling and statistics. The effects of noise (but probably mainly the systematic physical effects) cause small shifts in the designation of any given voxel as representing "this point in space at this instant in time." Really, any estimate of motion (or apparent motion) that is sub-pixel is an interpolation issue, and we see a lot of that in those relatively high frequency oscillations across the motion plots.<br /><br /> As for physiologic drifts with very low frequencies, yep, there are plenty. The origins could be varied, too, depending upon the nature of the experiment. I am preparing a blog post on the most common physiologic confounds in fMRI experiments. But on top of all these is the potential for slow neural effects. The MRI scanner is a soporific environment, I see no reason to exclude a priori the possibility of slow neural drifts with attention, with prolonged supine posture, etc. It all goes into the pot, and then we apply motion correction to it to try to tell us what's in the soup. Tricky!<br /><br />Cheers!<br /><br />practiCal fMRIhttps://www.blogger.com/profile/07387300671699742416noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-23473604536193185252014-10-19T18:25:42.983-07:002014-10-19T18:25:42.983-07:00I've spend a few weeks discovering this on my ...I've spend a few weeks discovering this on my own...running mcflirt on phantoms, making synthetic data. There's also the fundamental issue, that mcflirt is designed to align the same image to itself, not BOLD signal changed images to the reference. There's no built in regularization that I could see, to control for "motion" that is only BOLD signal change.<br /><br />Why should the phantom show motion...? It's not moving...the intensities may change along time, but there's no time axis in mcflirt. <br /><br />I found this today as well: http://www.ncbi.nlm.nih.gov/pubmed/19189286<br />Daniel Cuneonoreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-48984810366825049162013-09-26T19:02:18.268-07:002013-09-26T19:02:18.268-07:00You're correct, the thermal stability of ferro...You're correct, the thermal stability of ferrous material in the vicinity of an MRI is very important. Hence, as a general rule we don't like windows in the magnet room and if they must be included we do our best to avoid direct sunlight. Diurnal changes can be direct, from sunlight, and indirect, from use of HVAC and power anywhere else in the building (and assuming that you don't have the MRI on its own power conditioner). <br /><br />In academic environments especially, one also must consider effects in the other direction. I once had a small bore magnet relocated into a space with steel I-beams above. The beams went the length of the building where, at the other end, a lab had an electron microscope. The steel saturated immediately once the magnet was at field, and the lab's EM went waaaaaay out of spec. It was fixed but not before they had spent some time trying to figure out what on earth had silently and invisibly ruined their measurements!practiCal fMRIhttps://www.blogger.com/profile/07387300671699742416noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-69841174159312018122013-09-20T10:27:03.958-07:002013-09-20T10:27:03.958-07:00It's only taken me a about 2.5 years to stumbl...It's only taken me a about 2.5 years to stumble across this post, but I'm so glad I did!<br /><br />OK, first off, my physics is at a comparative Kindergarten level, so while I understand the basic principles, fully 80% of this sailed over my head, but what I did get reinforced site planning advice that I've been giving for years.<br /><br />The less steel you have in the magnet room construction (particularly the floor, as the closest part of the building to the magnet), the less passive shim material will be needed for that particular magnet. The less thermo-magnetic shim material there is, the less it can be subject to shift resulting from thermal gain.<br /><br />Granted more of my work is in clinical MRI settings than fMRI, or nMR spectroscopy, so I'm commenting on just a piece of the overall, I shudder when someone wants to place a clinical MRI system on top of a huge steel beam (which is the structural designer's first thought when you tell them you want to put a 10,000 kg load in the middle of the room). The magnet manufacturers have gotten better and better at shimming magnets that are place in lousy locations, so they've continuously relaxed their siting criteria. But we hear about magnets where doctors fight to get their patients in in the morning because image quality is noticeably poorer in the late afternoon (after 8 hours of duty cycles accumulating heat in the shim material). <br /><br />Siting your magnets smarter (with zero ferromagnetic material in the magnet room floor, if you can) help protects your data / image throughout the day. If you're spending a few million on a magnet, isn't it worth a few thousand to make sure that the the external influences (such as ferrous material and HVAC) are also set up to protect the quality of the data?Tobias Gilkhttps://www.blogger.com/profile/11962062084495006203noreply@blogger.com