tag:blogger.com,1999:blog-4402160631955197288.post7774903719531769572..comments2024-03-12T19:57:17.818-07:00Comments on practiCal fMRI: the nuts & bolts: Resting state fMRI - part IIIpractiCal fMRIhttp://www.blogger.com/profile/07387300671699742416noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-4402160631955197288.post-15994700835038288312011-05-17T11:28:15.035-07:002011-05-17T11:28:15.035-07:00@MCube: Ah, Montreal... I'm never drinking aga...@MCube: Ah, Montreal... I'm never drinking again :-|<br /><br />Echo Spacing/Bandwidth:<br /><br />On the Sequence card (Part 1) the Bandwidth (in Hz/Px) can be set in concert with the Echo spacing parameter. On a Trio you want to avoid 0.6-0.8 ms echo spacing for axial or axial oblique slices because of mechanical resonances in the X read gradient (which is L-R for the magnet). You could use an echo spacing in that range if there was no alternative, but the ghosting will be a bit higher. (I'll mention this factor again when I finally get to ghosting in my physics background series of posts.)<br /><br />In general (Trio, Allegra, whatever), use the lowest Bandwidth compatible with the echo spacing you select, because this minimizes the amount of ramp sampling versus sampling data on the flat portions of the read gradient episodes. (This also tends to reduce ghosts.) But, don't set bandwidth too low and make the echo spacing too long or distortion will get worse! For an Allegra I really couldn't say what's ideal, perhaps someone else reading the blog can comment? Failing that, you could run some tests on a phantom and evaluate the ghosts for various combinations of echo spacing and bandwidth, keeping your image matrix constant. If possible I would aim for an echo spacing down towards 0.5-0.56 ms for a 70x70 matrix and 210 mm FOV (for 3x3 mm pixels). <br /><br /><br />Oversampling:<br /><br />This is one of those things that comes out in the wash. You're using a small nominal FOV of 192 mm with oversampling. Alternatively, you could set up a larger FOV with proportionately larger matrix size and no oversampling, thereby maintaining the pixel size, and the pulse sequence timing parameters would be similar. You're not really gaining much in terms of performance, and with 3 mm voxels you're nowhere near to the physical limits of the system. In using a smaller FOV and oversampling you save a tiny bit of hard disk space (smaller images), and perhaps make your echo spacing a very small amount shorter, but at the expense of not having a true "noise" region around the head. (My preference is to have a small noise region in which to evaluate ghosts and other artifacts, which can be really hard to evaluate once almost the entire image is full of brain.) If you change the echo spacing and bandwidth appropriately, along with the FOV (larger) and matrix (larger) then you should see no effect on min. TE or on TR.<br /><br />Another concern with 192 mm FOV is that large heads and/or slight misplacement of slices could easily lead to you missing a portion of the brain completely! Much less of a risk with a 210 mm FOV. I'd be interested to know what the echo spacing and bandwidth can be set to with 3 mm voxels, FOV 210 mm, 70x70 matrix, no oversampling. I'll see if I can make a quick comparison on my Trio later today, I'm curious to see if there's a significant difference on my scanner now.<br /><br />Cheers!practiCal fMRIhttps://www.blogger.com/profile/07387300671699742416noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-62410125067216705102011-05-16T13:20:09.529-07:002011-05-16T13:20:09.529-07:00Hi Ben, I hope Montreal was fun!
So, thank you f...Hi Ben, I hope Montreal was fun! <br /><br />So, thank you for your suggestions. I think the oversampling ended up being the way to get the TR within 3s and the 3mm^3 resolution (and the matrix res above 64). I will go back to the hospital tomorrow so I should be able to play with the parameters a little more. If I get rid of the oversampling, won't I have to trade that off for a longer TR or larger voxels?<br /><br />Re the bandwidth, I was wondering about it. I didn't set it -- does the machine (it's an Allegra, not a TTrio) calculate that? If not, then I just inherited it from a previous sequence. I must confess though, I know what the bandwidth is, but I don't think I understand it's "consequences" well enough to find a 'better' value, so I'd like to know if you think there is a better one (or how can I go by finding it out..)<br /><br /> Let me know what your thought are -- and thank you, I wish there were many more physicists with whom I could talk (and actually understand what they are saying..!!)<br /><br />MCubeAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-65258097608816073512011-05-06T16:08:41.691-07:002011-05-06T16:08:41.691-07:00@MCube,
I'm not at the scanner and I'm...@MCube,<br /><br /> I'm not at the scanner and I'm away for the next week (ISMRM) so the first question is whether the 2604 Hz/Px bandwidth sits in a zone of mechanical resonance on your Trio. On mine (and others that I am familiar with), for axial or axial-obl slices (where X is read grad) we avoid 0.6-0.8 ms echo spacing to avoid mech resonances and above minimum ghosting. <br /><br />My next question: why the oversampling? This is equivalent to using a larger FOV and simply restricting the part of the image you want to view. As a matter of course I would always only acquire data points I want, so to maintain voxel size I would set no oversampling and reduce the phase encode matrix size proportionally. It all comes out in the wash, but as a general rule I don't know of a reason to oversample. It's equivalent (in terms of hardware performance needs) to using a larger FOV and matrix, and cropping the resultant image after FFT.<br /><br />Those two points are relatively benign. I think the rest of your params look perfectly reasonable too. If you have any residual concern about the interleaved no gap vs descending 5% gap (say), then I would suggest you acquire a couple of test data sets with the same 200 reps, back to back on a representative subject. Run the two data sets through your offline processing pipeline (especially realignment) as you'll use for your experiment, then generate TSNR maps. Locate the thalamus on either a raw EPI or on an MP-RAGE from the same session, and see which of the two slicing options is better, if at all.<br /><br />Re. motion generally, as I just informed another reader offline, tell the subject not to move if he hears the scanner going ping! Scratching nose, wiggling feet, stretching back etc can be done reasonably safely when the scanner is silent. (Re-shim if you want between EPI blocks - see last week's post.) In my experience ANY sort of body motion causes head motion, not just directly moving the head! Our necks will pitch with upper arm movement, leg movement, bum movement...practiCal fMRIhttps://www.blogger.com/profile/07387300671699742416noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-72315051771825322182011-05-06T11:00:49.749-07:002011-05-06T11:00:49.749-07:00Ben, thank you for the response. Yes true, for mot...Ben, thank you for the response. Yes true, for motion purposes descending is better, but because I am trying to go with no gap (I'm looking at thalamus, so resolution is precious..) interleaved seems the only way to go to avoid significant cross-talk (though, yes at the risk of big stripes in case of motion during a TR -- why do people not move only in the few msecs in-between TRs??).<br /><br />So, for comparison purposes, here is what I am trying to go with (though suggestions & criticisms are welcome):<br /><br />TR 3,000 ms (47 slices, 0 gap, interleaved)<br />TE 30 ms<br />FA 90<br />FOV read 192 mm (100% phase; 13% phase oversampling)<br />Vox size 3x3x3<br />(rel SNR = 1.00)<br />Repetitions 200<br />Base resolution 64<br />Bandwidth 2604 Hz/Px<br /><br />Sounds reasonable?<br /><br /> cheers<br /><br /> MCubeAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-57749790356905151572011-05-05T20:07:20.366-07:002011-05-05T20:07:20.366-07:00@Anonymous:
Yep, descending or ascending would wo...@Anonymous:<br /><br />Yep, descending or ascending would work (and is probably better in the presence of significant short-lived motion). But then you'd need between 5 and 20% gap (percent of slice thickness) to avoid cross-talk between adjacent slices. (In some tests I did ages ago I found that only 0% gap actually caused significant cross-talk.) Why the range of gap? Because of the side lobes and general trapezoidal nature of the slice profiles. Turns out it doesn't make that much difference for 2-4 mm slices. <br /><br />In sum, then, if you wanted the very best possible setting I'd suggest a 10% gap with descending or ascending slices. I used interleaved in these tests purely because I didn't remember to change it! (And in the absence of acute motion, which can cause stripes in the slice dimension with interleaved slices due to perturbation of the T1 steady state, it doesn't matter that much. I was the subject and I was careful not to move!)practiCal fMRIhttps://www.blogger.com/profile/07387300671699742416noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-18249073811680090082011-05-05T13:43:38.116-07:002011-05-05T13:43:38.116-07:00Well, one question is the gap. Why use it and not ...Well, one question is the gap. Why use it and not do a descending interleaved with no gap?<br />Thank you for the post, very interesting!<br /><br /> cheers<br /><br /> MCubeAnonymousnoreply@blogger.com