Yeah, upon hearing about PURE correction I had high hopes, but it works less well than it sounds. The B1 field mapping sequence on DV24 is a bit funny apparently; I'll let you know what our sequence programmer is able to come up with
__________________________ gaurav patel gauravpa...@gmail.com www.neurofreak.net On Jun 3, 2015, at 2:57 PM, Barbara Kreilkamp wrote: > Dear Gaurav and Matt, > > I found out that the 32-channel head coil we use is only for receiving > signal, it does not provide the radiofrequency transmit, the body coil does. > The GE physicist responded to explain the functionality of PURE: "Pure use > the calibration scan to map the coil element sensitivity first (->calibration > scan) and correct for the signal drop off retrospectively based on this." > > He also said there should be a B1-Field map sequence ready to use under > 'DV24' (Bloch Siegart method). I'll see when I can get the team to acquire it. > Thank you for this helpful exchange! > > All the best wishes, > Barbara > > On 01/06/2015 18:19, Gaurav Patel wrote: >> 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. 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