I also spoke to our sequence programmer about getting B1 receive and transmit field measurements here, and he said he thought we had the necessary sequences. I'll let you know what happens
__________________________ gaurav patel gauravpa...@gmail.com www.neurofreak.net On Jun 1, 2015, at 1:09 PM, Barbara Kreilkamp wrote: > Yes, thank you for this Matt, I'll see if I can get the team here to > acquire a transmit field map, though I can't promise, as we're scanning > at a hospital. > Cheers, > Barbara > > On 01/06/2015 18:06, Glasser, Matthew wrote: >> So the medial part gets fixed by the BC stage, but the lateral part >> doesn¹t. I think we¹ll need to find out more about the transmit field, as >> that is likely the issue. >> >> Matt. >> >> On 6/1/15, 11:48 AM, "Barbara Kreilkamp" <bakk....@googlemail.com> wrote: >> >>> Thank you so much to both of you. >>> Online I also found the information that XETA and CUBE would be the same >>> sequences - Aiken et al. 2011 (American Journal of Neuroradiology) and >>> Moseley et al. 2009 (Neurologic clinics). >>> I really need to consult with the GE physicists to be able to answer >>> these questions. I'll let you know what I find out. >>> Matt, for now I am attaching the myelin maps without _BC in the >>> filename, for the same subject. Do they look like what you would have >>> expected? >>> >>> Thank you, >>> Best wishes, >>> Barbara >>> >>> >>> >>> >>> On 31/05/2015 22:26, Gaurav Patel wrote: >>>> We¹ve looked fairly extensively at this issue, and have learned a few >>>> things: >>>> >>>> 1) The T2 XETA used in the NAMIC was just a preproduction version of >>>> the sequence later called CUBE, so there is no real difference (this is >>>> per Sylvain Bouix, who was part of the NAMIC data collection). I just >>>> emailed him back to get the dicom header for the SPGR used in the NAMIC >>>> data set to see if there are any differences between it and our FSPGR. >>>> >>>> 2) We initially used a 32 channel NOVA coil for data collection, but in >>>> an effort to replicate the NAMIC dataset as closely as possible we also >>>> tried the GE 8 channel coil; while it reduced the artifact it was still >>>> present. (The transmit coil was the body coil in both cases). >>>> >>>> 3) PURE correction also doesn¹t adequately compensate for the artifact. >>>> I forget what exactly happened, but when I¹m at work tomorrow I¹ll dig >>>> up the images and send them along. >>>> >>>> 4) Post-recon inhomogeneity correction also doesn¹t do the trick. I >>>> used both ANTS and FAST (both with and without brain masking) and wasn¹t >>>> able to fully deal with the issue. Often what happened was that the >>>> artifact ³reversed² in that after correction the edge of the brain had >>>> artifactually boosted T1/T2 ratio rather than the middle of the brain. >>>> >>>> >>>> In addition we had some ringing artifact in the T2s that we found was >>>> caused by the GE scanner¹s default behavior of reconstructing the images >>>> in a different matrix size than the acquisition, and in the course of >>>> our testing found a set of parameters that seemed to increase G/W >>>> contrast in the T2. I can pass those parameters along also when I¹m >>>> back at my desk. There is a mythical GE version of the MPRAGE thats >>>> floating around somewhere, but we haven¹t been able to get our hands on >>>> it yet. If anyone has one we¹d be happy to do some testing with it. >>>> Unfortunately GE themselves has been less the helpful on this issue >>>> (amongst others) but perhaps if there are enough of us knocking on their >>>> door they¹ll be of more help. >>>> >>>> At some point I¹m going to run a test on a phillips scanner that we >>>> have at Columbia where there is an MPRAGE; I¹ll let you know how that >>>> works out. At this point though I don¹t feel confident that the myelin >>>> map data we¹ve collected so far is worth much; I had been hoping that >>>> inhomogeneity correction would help but it hasn¹t so far. Again any >>>> other insight would be appreciated. >>>> >>>> >>>> __________________________ >>>> gaurav patel >>>> gauravpa...@gmail.com >>>> www.neurofreak.net >>>> >>>> >>>> >>>> >>>>> On May 31, 2015, at 4:21 PM, Glasser, Matthew >>>>> <glass...@wusm.wustl.edu> wrote: >>>>> >>>>> Hi Barbara, >>>>> >>>>> I agree that the main heavily myelinated areas are found, the issue is >>>>> with that lateral cortex (e.g. the difference between STG and STS is a >>>>> lot higher than we see). >>>>> >>>>> Do you know how the PURE correction is computed? We generally avoid >>>>> these sorts of automatic corrections (even Siemens pre-scan normalize, >>>>> for which we know what it is doing), and the HCP pipelines don¹t >>>>> require receive fields to be corrected for ahead of time (though they >>>>> shouldn¹t mind if the same correction is done to both T1w and T2w >>>>> images). If the PURE correction is not based on acquiring additional >>>>> images that can be used to directly measure the receive field, it could >>>>> well do something different to the T1w and T2w images. I don¹t know if >>>>> Gaurav is using the PURE correction though. >>>>> >>>>> My question about the head coil was more specific than if you used >>>>> one: Did it provide the radio frequency transmit or was it just used to >>>>> receive radio frequency? >>>>> >>>>> I¹m not sure what you¹re doing with the data, so I can¹t say whether >>>>> it is usuable or not. You wouldn¹t be able to directly compare >>>>> subjects acquired on Siemens to those acquired on GE, and you¹d need to >>>>> be careful interpreting the neuroanatomy (strangely the medial surface >>>>> looks just fineŠ). Can you post the myelin map data without the _BC on >>>>> it so I can see what that looks like? >>>>> >>>>> Unfortunately sorting this issue out may require consultation with the >>>>> GE MR physicists to understand why their scanners are behaving >>>>> strangely here. A spatial map of the flip angles or transmit field >>>>> produced by this scanner might also be informative. >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> From: Barbara Kreilkamp <bakk....@googlemail.com> >>>>> Date: Sunday, May 31, 2015 at 3:01 PM >>>>> To: Matt Glasser <glass...@wusm.wustl.edu>, Gaurav Patel >>>>> <gauravpa...@gmail.com>, "hcp-users@humanconnectome.org" >>>>> <hcp-users@humanconnectome.org> >>>>> Subject: Re: [HCP-Users] myelin maps on GE scanner >>>>> >>>>> Thank you Matt for this expert advice. >>>>> I've checked FNIRT registration for this subject, and it seemed fine, >>>>> to make sure the high/low intensities in the myelin map were not >>>>> generated through poor registration between T1 FSPGR BRAVO and T2 CUBE. >>>>> So, which areas are we worried about in particular - the superior >>>>> temporal sulcus for example? The patterns in motor cortex and V1 seem >>>>> to resemble your images? >>>>> We had real problems with inhomogeneity on the 3T GE scanner, but we >>>>> applied the PURE intensity corrections and I computed a significant >>>>> decrease of the bias field, when comparing those images to T1s without >>>>> PURE correction. >>>>> Yes, we used a head coil. >>>>> Do you think we'd have to bid farewell to a myelin mapping approach >>>>> with this data or would you say there is a work-around by doing >>>>> ROI-analysis etc.? >>>>> >>>>> Thanks, >>>>> Best wishes, >>>>> Barbara >>>>> >>>>> >>>>> >>>>> On 31/05/2015 20:42, Glasser, Matthew wrote: >>>>>> Hi Barbara, >>>>>> >>>>>> Unfortunately those actually look much more like Gaurav¹s than the >>>>>> ones in in Figure 3 of Glasser and Van Essen 2011 (panels B, E, H, K >>>>>> were from a GE scanner). The issue is that the sulci on the lateral >>>>>> surface are brighter than the gyri in a noticeable way relative to >>>>>> what we typically see, which is not something we saw in the NAMIC GE >>>>>> data or any of our Siemens data over the years. I¹m quite puzzled by >>>>>> this issue, since it the myelin maps used to work on GE and give >>>>>> comparable results to Siemens. Also, I don¹t have any experience with >>>>>> GE scanners to know what parameters might be creating the issue. >>>>>> >>>>>> Here is the info that was available for the GE NAMIC data (that was >>>>>> acquire some time ago now): >>>>>> >>>>>> The second dataset includes the 10 control subjects (all male, mean >>>>>> age ? 42 ? 11 years) from the publicly available Brain Multimodality >>>>>> dataset from the National Alliance for Medical Image Computing (NAMIC) >>>>>> (provided by the Psychiatry Neuroimaging Laboratory and the Surgical >>>>>> Planning Laboratory, Brigham and Women¹s Hospital). The data were >>>>>> acquired on a 3T General Electric (GE) scanner at Brigham and Women¹s >>>>>> Hospital in Boston using an 8-channel head coil and GE¹s parallel >>>>>> imaging technology Array Spatial Sensitivity Encoding Techniques >>>>>> (ASSET) was used with a SENSE (SENSitivity Encoding) factor of 2. A >>>>>> T1w spoiled gradient recalled sequence (SPGR; TR ? 7.4 ms, TE 3 ms, >>>>>> TI?600 ms, 10° flip angle, FOV 256mm?256 mm, matrix 256? 256, 1 mm >>>>>> slices) and a T2w extended echo train acquisition (XETA; TR?2500 ms, >>>>>> TE?80 ms, FOV 256mm?256 mm, matrix 256?256, 1 mm slices) were >>>>>> acquired. Data were downloaded from the NAMIC MIDAS website: >>>>>> http://insight-journal.org/midas/collection/view/190. >>>>>> >>>>>> I¹d actually be more inclined to suspect that the T2w sequence >>>>>> difference CUBE vs the XETA might be the cause of the issue. On >>>>>> Siemens we use a T2w SPACE sequence which has a lot of contrast for >>>>>> myelin in it (T2w being a bit of a misnomer, as the contrast in the >>>>>> SPACE is mostly T1 and MT), if the T2w scan were to have less contrast >>>>>> for myelin, that could reduce the quality of the results. Another >>>>>> possibility would be if the transmit field is substantially more >>>>>> inhomogeneous on this GE scanner (which is probably a different model >>>>>> than the one used for the NAMIC data). Is the transmit done from a >>>>>> body coil or a head coil for this GE scanner? In the Siemens scanners >>>>>> we use the more uniform transmit from the body coil, but if the head >>>>>> coil were used for transmit, it could produce a more inhomogeneous >>>>>> field. >>>>>> >>>>>> Peace, >>>>>> >>>>>> Matt. >>>>>> >>>>>> From: Barbara Kreilkamp <bakk....@googlemail.com> >>>>>> Date: Sunday, May 31, 2015 at 2:25 PM >>>>>> To: Gaurav Patel <gauravpa...@gmail.com>, >>>>>> "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>>>> Subject: Re: [HCP-Users] myelin maps on GE scanner >>>>>> >>>>>> Hi Gaurav, >>>>>> >>>>>> Could you please send over a screenshot of what the artifacts look >>>>>> like? >>>>>> We've acquired 3D FSPGR BRAVO with PURE correction on the GE MR750 >>>>>> Discovery 3T together with 3D CUBE with PURE correction (32 channels). >>>>>> The images that HCP computed from that for me look very much like the >>>>>> ones from Matt's publication, Neuroimage 2014 (single subject), >>>>>> scaling is 4% to 96% (attached). >>>>>> Please let me know if this helps or if I can help in any other way. >>>>>> >>>>>> Thanks, >>>>>> Best wishes, >>>>>> Barbara >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 30/05/2015 17:53, Gaurav Patel wrote: >>>>>>> Another problem we have been having is artifacts in myelin maps >>>>>>> generated from the T1s and T2s acquired on our GE MR750D 3T magnet. >>>>>>> Matt and I looked at this in December, and found that in our maps >>>>>>> there tended to be an artifactual bias towards increasing T1/T2 ratio >>>>>>> towards the center of the brain, leading to apparent dense >>>>>>> myelination depp in sulci and light myelination at the tops of sulci >>>>>>> that were not real. We've been trying to get to the bottom of this >>>>>>> problem since then with no luck, so I'm turning to the list to see if >>>>>>> anyone else has successfully created myelin maps on a GE scanner and >>>>>>> would be willing to share their sequences (or at least parameters). >>>>>>> We've traced the problem (we think) to the difference between the >>>>>>> FSPGR that GE scanners use and the MPRAGE, specifically the inversion >>>>>>> pulse that seems to make the FSPGR more sensitive to B1 receive field >>>>>>> inhomogeneity than the MPRAGE (and the T2 sequence, hence the bias in >>>>>>> the T1/T2 ratio). We' >>>>>>> ve compar >>>>>>> ed our seq >>>>>>> uence to the one used in the NAMIC dataset obtained on an older GE >>>>>>> scanner that Matt used in his original myelin mapping paper and >>>>>>> haven't come up with any real differences so far. Any help or >>>>>>> insight would be appreciated. Thanks! >>>>>>> >>>>>>> __________________________ >>>>>>> gaurav patel >>>>>>> >>>>>>> gauravpa...@gmail.com >>>>>>> >>>>>>> >>>>>>> www.neurofreak.net >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> HCP-Users mailing list >>>>>>> >>>>>>> >>>>>>> HCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/ >>>>>>> listinfo/hcp-users >>>>>> _______________________________________________ >>>>>> HCP-Users mailing list >>>>>> HCP-Users@humanconnectome.org >>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>>> >>>>>> The materials in this message are private and may contain Protected >>>>>> Healthcare Information or other information of a sensitive nature. If >>>>>> you are not the intended recipient, be advised that any unauthorized >>>>>> use, disclosure, copying or the taking of any action in reliance on >>>>>> the contents of this information is strictly prohibited. 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