Re: [HCP-Users] myelin maps on GE scanner
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" 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 > 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 >
Re: [HCP-Users] myelin maps on GE scanner
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" 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 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 subjec
Re: [HCP-Users] myelin maps on GE scanner
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" 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 >>> 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 a
