tag:blogger.com,1999:blog-4402160631955197288.comments2024-03-12T19:57:17.818-07:00practiCal fMRI: the nuts & boltspractiCal fMRIhttp://www.blogger.com/profile/07387300671699742416noreply@blogger.comBlogger372125tag:blogger.com,1999:blog-4402160631955197288.post-7815422019241733722024-02-01T07:14:41.699-08:002024-02-01T07:14:41.699-08:00great articlegreat articleSaif Shahabhttps://www.blogger.com/profile/13314285952091915562noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-21298390346782529522023-07-05T15:11:28.526-07:002023-07-05T15:11:28.526-07:002023 and these posts are still helpful! thanks aga...2023 and these posts are still helpful! thanks again for doing theseAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-49560108376724489862023-06-04T16:47:46.944-07:002023-06-04T16:47:46.944-07:00Sorry, not worked in this space for some time. I s...Sorry, not worked in this space for some time. I still wouldn't go beyond MB=6 under almost any circumstances, and I'd try to limit the factor to the number of planes of loops in the coil (around four for a 32ch coil, perhaps five or six in the 64ch coil). I'd also not do in-plane GRAPPA unless you have robust tactics to ensure you don't get corrupted ACS. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-16180818666462516012023-03-11T12:27:43.874-08:002023-03-11T12:27:43.874-08:00Proper communication of safety protocols and rehea...Proper communication of safety protocols and rehearsals are required to be updated in physical practice in conjunction with Radiology, Nursing staff, Clients (Patients) and Public in a quarterly scheduling.<br />I also appreciate how challenging this exercise would be to management in terms of resources.<br />Priorities safety at all cost.<br /><br /><br />Timothy Isaiah Kumwendanoreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-75353093465509462332022-08-24T16:50:56.499-07:002022-08-24T16:50:56.499-07:00Same way as given in Note 2 :-) It all depends on ...Same way as given in Note 2 :-) It all depends on the EPI time series you load into the viewing window for subsequent analysis. Just load from the Patient Browser the PACE MOCO time series you want to evaluate. If you have the pre- and post-MOCO data available then you can evaluate each time series in turn and compare.practiCal fMRIhttps://www.blogger.com/profile/07387300671699742416noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-15866180564950763732022-08-24T16:48:07.409-07:002022-08-24T16:48:07.409-07:00Really sorry for the lengthy delay, I haven't ...Really sorry for the lengthy delay, I haven't been near by blog for some time! <br /><br />I think you have misunderstood chemical shift hence chem shift artifacts. The CSA isn't the sum of the water and fat signals. The fat signals resonate at a different frequency (circa 700 Hz away) from water. Since we use frequency encoding to establish the spatial parameters in the image, this ~700 Hz offset means an image of fat will appear a few pixels displaced from an image of water. This is true whether the fat or water signals are intense or weak. But if the fat signals happen to be intense then the displaced image can be a significant distraction and, for diffusion imaging specifically, where the fat image overlaps the water image can produce false 'tracts' in the data that have nothing to do with water translational diffusion.practiCal fMRIhttps://www.blogger.com/profile/07387300671699742416noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-32337446260972903062022-08-24T16:42:30.524-07:002022-08-24T16:42:30.524-07:00Hi Joe, if I had said "the distance between s...Hi Joe, if I had said "the distance between successive frequency-encoded rows" instead of "lines," would that help clarify? Yes, each frequency-encoded line (or row) is being phase-encoded, what is important in the sentence you flagged is the initial part, the "distance between." It's the step size in the column direction that is important. Delta-k (phase) is the same for partial k-space as full k-space, so the final field-of-view is the same in these two cases.practiCal fMRIhttps://www.blogger.com/profile/07387300671699742416noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-54584084617902278362022-08-24T11:23:36.401-07:002022-08-24T11:23:36.401-07:00Hi Tamer, we came across the issue first in relati...Hi Tamer, we came across the issue first in relation to custom printed head restraint but yes, in principle it can happen with any sort of head restraint, even foam. The first part of the problem is that pushing the coil all the way to the back of the bed where it is least likely to move will place some strain on the front connectors. If the subject's head motion is well coupled to the upper part of the coil, e.g. because you have a lot of foam packing, then those front connectors can wiggle. Generally, however, most subjects can still move their head vs the foam packing and not move the coil. The anti-slip pads on the bottom of the coil also reduce the likelihood of the coil moving. So the bottom line is that the better you restrain the subject's head, the greater the concern that the coil might now move instead.practiCal fMRIhttps://www.blogger.com/profile/07387300671699742416noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-36232164533751330902022-07-27T12:40:32.602-07:002022-07-27T12:40:32.602-07:00Hi,
Our scanner and head coil is the same as the ...Hi,<br /><br />Our scanner and head coil is the same as the one on the picture. Is this issue relevant to for those who use a custom head restraint or is it a general issue which will exhibit itself when participants are restrained with foam pads as well? I am not sure what you mean by "custom head restraint" here so I needed to ask. When we tried the head coil and placed it in place (without running a scan) and tried wiggling it in the direction towards (inside) the bore we found that there was room for motion, but that much motion done by a participant's head would already lead to lots of other problems apart from the movement of the coil. Would the vibrations of the scanner affect things that much? And what kind of tests can be do to check if this issue is indeed there.Tamernoreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-45643540416375881712022-07-11T10:30:23.169-07:002022-07-11T10:30:23.169-07:00thanks so much and learned a lot from your blogs. ...thanks so much and learned a lot from your blogs. Is this typo "the distance between successive frequency-encoded lines of k-space is exactly as was demonstrated in earlier posts on EPI."? should it be phase-encoded lines instead? joe.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-48358987296714074272021-12-21T11:03:11.301-08:002021-12-21T11:03:11.301-08:00Hi, I'm a staff scientist for the neuroimaging...Hi, I'm a staff scientist for the neuroimaging community at the University of Arizona. We are developing a neuroimaging certificate to provide graduate students with just the sort of training you are talking about. My colleague will teach fMRI design and analysis, I'll teach computational skills (Unix, BIDS, datalad etc.). I think we are motivated by exactly the same issues that you are, and I appreciate the way you described it. I look forward to hearing more...Dianne Pattersonhttps://www.blogger.com/profile/12437494322330186454noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-34432654924108823242021-12-15T18:36:36.829-08:002021-12-15T18:36:36.829-08:00I am potentially interested in this effort. Partly...I am potentially interested in this effort. Partly because I agree that I often see that many experiences and tips are hard to be passed on to the next generation researchers and mistakes are made repeatedly in every generation, partly because I also want to refresh myself on some of the topics.Mingbo Caihttps://cailab-ircn.org/noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-50627063125245557252021-12-14T08:42:53.403-08:002021-12-14T08:42:53.403-08:00This sounds like a great plan. Happy to help where...This sounds like a great plan. Happy to help where and when I can.satrahttps://www.blogger.com/profile/11229619739867347865noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-30012276876359950882020-10-28T20:51:47.598-07:002020-10-28T20:51:47.598-07:00Thank you for a great post! I would like to ask an...Thank you for a great post! I would like to ask an elementary question. According to the post, signal intensity of chemical shift artifacts, i.e., the sum of water and fat signals, can be high intensity or low intensity compared to the water signal. In the case of high intensity, it is quite intuitive to me. That is, if the water signal and the fat signal are 100 and 10, respectively, then the signal of chemical shift artifact is 110, which is a high signal relative to the water. On the other hand, what I do not understand is the case of a low signal case. For example, if the signal of the water is 100 and the signal of the artifact (water and fat) is 90, then the signal of the fat must be -10, i.e., a negative signal. How should we interpret this negative signal??<br /><br />Seina from JapanAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-5894497232888074582020-10-20T07:56:31.410-07:002020-10-20T07:56:31.410-07:00Thank you for this interesting analysis.
I'm ...Thank you for this interesting analysis.<br /><br />I'm currently running similar tests using the body-18 wrapped around an extremity. Some may want to run DTI in the muscle for example. Given that this coil is 18 channels arranged in a staggered 3x6 configuration (also Tim), it gives similar results to your 4 channel at MB=2. There is subtle aliasing on a bottle, but nothing noticeable on actual anatomy. This is on a Prisma and I turned of matrix optimization. Multiple averages are required however in this area. Still, our pilot scans and analysis indicate that at least for MB=2 you can achieve acceptable quality with good tractography.fmri_canhttps://www.blogger.com/profile/13492053768410351929noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-40235462939929011222020-05-04T11:32:21.240-07:002020-05-04T11:32:21.240-07:00Can you tell me how to calculate tSNR for Siemens ...Can you tell me how to calculate tSNR for Siemens PACE MOCO?Kristihttps://www.blogger.com/profile/05800218441776493273noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-30146436036355962112020-02-19T12:17:05.123-08:002020-02-19T12:17:05.123-08:00Hi, I'm trying to adapt biobank's dMRI seq...Hi, I'm trying to adapt biobank's dMRI sequence on our Siemens Trio (software VB19) with a 32 channel head coil and the CMRR-MB. <br />I know this might not be the right place to ask but I am having some problems with the following issues and I was wondering if you could help me:<br /><br />- In the special tab I don't get the option for the SENSE1 coil combine ("sum of squares" coil combine mode is selected in the System tab), am I missing something?<br /><br />- With the Trio I get a minimum echo spacing of 0.69ms for this sequence (vs 0.67ms of the original sequence, developed on a Skyra), with longer TE (96.4ms vs 92ms) and greater distortion and signal dropout. Any tips on which is the best strategy to lower the TE and address this issue?<br /><br />Thanks in advance for your help!<br /><br />Regards,<br />GiuseppeGiuseppehttps://www.blogger.com/profile/07266401060442981367noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-12695170109754918512019-11-05T23:39:41.533-08:002019-11-05T23:39:41.533-08:00This comment has been removed by the author.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-45412464223218758102019-08-06T08:50:07.300-07:002019-08-06T08:50:07.300-07:00Not looked at this issue for some time, I'm af...Not looked at this issue for some time, I'm afraid. For voxel sizes smaller than 2mm, people at my center have adopted the TOPUP approach using the SE-MB-EPI with two phase encoding directions, mostly because of the long acquisition time needed for a true field map. I do still have a few people using true field maps, but only for larger than 2mm voxels. I also have people doing diffusion imaging with MB who have 2mm voxels and still opt for TOPUP, again for time.practiCal fMRIhttps://www.blogger.com/profile/07387300671699742416noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-90224016554294958252019-08-06T00:58:40.520-07:002019-08-06T00:58:40.520-07:00Hi! I wanted to ask whether there is any update on...Hi! I wanted to ask whether there is any update on the issue with the spatial resolution of the fieldmap / Spin Echo field maps you mention in this post. We are running into the same issue (fixed lower limit on slice thickness) with the Siemens product and the CMRR Spin Echo field maps. Thanks! cmshttp://www.eni-g.de/groups/neural-circuits-and-cognitionnoreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-4743218879878249542019-03-20T09:28:27.349-07:002019-03-20T09:28:27.349-07:00Yes, always! :-)Yes, always! :-)practiCal fMRIhttps://www.blogger.com/profile/07387300671699742416noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-9265643657796271352019-03-20T09:11:22.116-07:002019-03-20T09:11:22.116-07:00Hi - thanks, v useful as always! One question (and...Hi - thanks, v useful as always! One question (and apologies if this info is included above and I missed it): did you do these tests (fMRI and diffusion) with in-plane iPAT turned off?David Thomashttps://www.blogger.com/profile/03587566319069876681noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-61692480036072242322019-03-01T08:35:00.482-08:002019-03-01T08:35:00.482-08:00"In the past, Siemens product DTI sequences a..."In the past, Siemens product DTI sequences always used a refocusing pulse (aka bipolar) sequence."<br /><br />Oh! I didn't know that. Do you know if this is related to their recent shift to enabling the Prescan Normalize option on all product DTI protocols? This seemed to happen with the release of VE11 software. I first heard about it in relation to a PRISMA, and wondered if it was a way to make cosmetic improvements for their 64ch coil option; to avoid scaring users with the strong receive field heterogeneity in the raw data. But I also wondered about eddy currents, since normalizing the Rx field might improve offline eddy current compensation via e.g. EDDY, because otherwise the EDDY routine may not differentiate true anatomical contrast (desired performance) versus "features" introduced by the Rx bias field (undesirable performance). This is the same argument for using normalized images for volume realignment when doing motion correction in fMRI acquired on large array coils: see https://practicalfmri.blogspot.com/2012/11/review-using-bias-field-map-to-improve.htmlpractiCal fMRIhttps://www.blogger.com/profile/07387300671699742416noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-19040155359330055002019-03-01T05:22:07.193-08:002019-03-01T05:22:07.193-08:00We conducted a similar evaluation with our Prisma ...We conducted a similar evaluation with our Prisma using the 20-channel head-neck coil.<br /> https://osf.io/brvak/<br />I do have a couple comments:<br /> 1.) In the past, Siemens product DTI sequences always used a refocusing pulse (aka bipolar) sequence. The bipolar sequence reduces spatial distortion and provides better control for back ground gradients. However, as you note bipolar sequences have high SAR and they also require long echo times (which reduces SNR). The recent Siemens product sequences as well as the excellent CMRR sequences allow you to select either a monopolar or a bipolar sequence. Using TOPUP/Eddy you can remove a lot of the spatial distortion associated with monopolar sequences. This is one reason we directly tested monopolar versus bipolar.<br /> 2.) We also describe how to quantify the signal to noise in a DWI scan. I think it is important to visually inspect for multi-band artifacts, having an empirical method to assess overall SNR is really useful when selecting between the many trade offs of different DWI sequences.Unknownhttps://www.blogger.com/profile/00393372454805882868noreply@blogger.comtag:blogger.com,1999:blog-4402160631955197288.post-1575997293503135072019-02-23T06:16:35.624-08:002019-02-23T06:16:35.624-08:00Sample 20 channel (MB=2,3,4,5) and 32 channel (MB=...Sample 20 channel (MB=2,3,4,5) and 32 channel (MB=2,5) from a human volunteer and 100 volumes are provided here: https://osf.io/q4d53/<br />I would be interested in any thoughts.Unknownhttps://www.blogger.com/profile/00393372454805882868noreply@blogger.com