A>>P Thanks
Regards --VM On Thu, Dec 8, 2016 at 1:40 PM, Glasser, Matthew <[email protected]> wrote: > What phase encoding directions are you using? > > Peace, > > Matt. > > From: neuroimage analyst <[email protected]> > Date: Thursday, December 8, 2016 at 1:37 PM > To: "Harms, Michael" <[email protected]> > Cc: Matt Glasser <[email protected]>, "[email protected]" < > [email protected]> > Subject: Re: [HCP-Users] FW: Skyra - BOLD and diffusion MRI protocols > > Hi, > > Just an update: > > 1) BOLD: I was able to run the sequence with all the parameters as > mentioned but with the resolution of 2.5mm3 and Partial fourier 7/8. I was > unable to decrease the resolution with that Partial Fourier factor of > anything or resolution of 2.5mm3 with no partial fourier. I will scan a > subject today and see how the data looks. > > 2) dMRI: MB factor = 3. RF pulse clipping issue was resolved. TR is 5600 > and TE is 100 ms , 2 b-values and 71 diffusion encoding directions running > under free mode. Resolution of 1.5mm3; scan time of 15 mins. I added a PA > phase encoding with 2 averages of b0. Again, I will test the sequence with > a subject and different resolutions to see if the data is acceptable. > > Thank you for all your help and advice/suggestions. > > Regards > > --VM > > On Wed, Dec 7, 2016 at 12:31 PM, Harms, Michael <[email protected]> wrote: > >> >> Oh. I read too quickly and conflated the problem you were having for the >> BOLD with the dMRI. So, you can set up a BOLD scan with those parameters, >> and it only fails at run-time? Can you achieve a higher MB factor if you >> relax the spatial resolution to say 2.4 mm. (Although that shouldn’t be >> necessary, because it is possible to do 2.0 mm, MB=8 BOLD on a Trio). You >> might have to ask the CMRR folks via their github issues page: >> https://github.com/CMRR-C2P/MB/issues >> >> Regarding the dMRI: What MB factor were you using there? And did you >> resolve the issue with the RF pulse clipping? (Either by lengthening the >> pulses further (within reason), or you could try using the “MB RF phase >> scramble” option; and if that isn’t sufficient, try the “Time-shifted MB >> RF” option as well). >> >> cheers, >> -MH >> >> -- >> Michael Harms, Ph.D. >> ----------------------------------------------------------- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave.Tel: 314-747-6173 <(314)%20747-6173> >> St. Louis, MO 63110Email: [email protected] >> >> From: neuroimage analyst <[email protected]> >> Date: Wednesday, December 7, 2016 at 1:54 PM >> To: Michael Harms <[email protected]> >> Cc: "Glasser, Matthew" <[email protected]>, " >> [email protected]" <[email protected]> >> Subject: Re: [HCP-Users] FW: Skyra - BOLD and diffusion MRI protocols >> >> I apologize for not making the question very clear. I think I have sort >> of optimized the diffusion protocol the way I wanted it to be. I just need >> to do a human scan and compare SNR between different resolutions to see the >> limit where i can get acceptable data. >> >> The issue that I am unable to solve is this: >> BOLD: We were hoping to get a TR in the range of 750-900ms, res = 2mm3, >> echo spacing (ES) approx 0.65. We were able to get to echo spacing of 0.69 >> and all the other parameters with MB = 8. However, the sequence doesn't run >> and it gives us "Max amplitude overflow on gradient z axis" after MB factor >> exceeds 2. It appears to me that then we have to sacrifice TR and only run >> with MB = 2. We are using 32 channel head coil. >> >> Thank you for any suggestions. >> >> Regards >> >> Virendra >> >> On Wed, Dec 7, 2016 at 11:22 AM, Harms, Michael <[email protected]> wrote: >> >>> >>> I wouldn’t think that increasing the MB factor would increase the >>> gradient requirements that much, so I’m wondering if trying to run with >>> b_max = 2500 isn’t at the very edge of what can be achieved on the Skyra >>> for that particular gradient direction set. What happens if you lower the >>> b_max to say 1500? Can you then increase the MB factor without getting >>> that error? >>> >>> -- >>> Michael Harms, Ph.D. >>> ----------------------------------------------------------- >>> Conte Center for the Neuroscience of Mental Disorders >>> Washington University School of Medicine >>> Department of Psychiatry, Box 8134 >>> 660 South Euclid Ave.Tel: 314-747-6173 <(314)%20747-6173> >>> St. Louis, MO 63110Email: [email protected] >>> >>> From: neuroimage analyst <[email protected]> >>> Date: Wednesday, December 7, 2016 at 1:03 PM >>> To: Michael Harms <[email protected]> >>> Cc: "Glasser, Matthew" <[email protected]>, " >>> [email protected]" <[email protected]> >>> Subject: Re: [HCP-Users] FW: Skyra - BOLD and diffusion MRI protocols >>> >>> Thanks for that reply, Micahel. Exactly, what I plan to do for diffusion >>> protocol. >>> >>> Just wondering though on your or anyone else's suggestion on running >>> BOLD with MB>2. >>> >>> Thanks >>> >>> Regards >>> >>> --VM >>> >>> >>> On Wed, Dec 7, 2016 at 10:50 AM, Harms, Michael <[email protected]> >>> wrote: >>> >>>> >>>> Hi, >>>> It appears that you are trying to replicate the basics of one of our >>>> Lifespan pilot protocols on a Skyra — i.e., 1.5 mm voxels with 20 total min >>>> of dMRI scanning. But due to the longer TE and longer TR (resulting in >>>> fewer total directions), you are definitely going to have worse overall SNR >>>> than what we achieved. We highly suggest that you collect some pilot data >>>> to assess the quality of your proposed dMRI protocol with your end-measures >>>> of interest, including possibly a comparison against a protocol with larger >>>> voxels (e.g., 1.7-1.8 mm voxels) that would recover some SNR. >>>> >>>> cheers, >>>> -MH >>>> >>>> -- >>>> Michael Harms, Ph.D. >>>> ----------------------------------------------------------- >>>> Conte Center for the Neuroscience of Mental Disorders >>>> Washington University School of Medicine >>>> Department of Psychiatry, Box 8134 >>>> 660 South Euclid Ave.Tel: 314-747-6173 <(314)%20747-6173> >>>> St. Louis, MO 63110Email: [email protected] >>>> >>>> From: <[email protected]> on behalf of "Glasser, >>>> Matthew" <[email protected]> >>>> Date: Wednesday, December 7, 2016 at 11:49 AM >>>> To: "[email protected]" <[email protected]> >>>> Subject: [HCP-Users] FW: Skyra - BOLD and diffusion MRI protocols >>>> >>>> >>>> >>>> From: Matt Glasser <[email protected]> >>>> Date: Wednesday, December 7, 2016 at 10:14 AM >>>> To: neuroimage analyst <[email protected]> >>>> Subject: Re: [HCP-Users] Skyra - BOLD and diffusion MRI protocols >>>> >>>> I wouldn’t acquire multiple repetitions of the same directions, but >>>> rather more unique directions. If necessary you can acquire the DWIs with >>>> only a single phase encoding direction in an effort to get more unique >>>> diffusion directions, but it is important that you get phase reversed b0 >>>> images. >>>> >>>> As for the MB error, I don’t know how to fix it, but you should >>>> definitely be able to do better than MB=2 with a 32 channel head coil. >>>> Hopefully someone else on the list knows how to fix this. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: neuroimage analyst <[email protected]> >>>> Date: Tuesday, December 6, 2016 at 8:54 PM >>>> To: Matt Glasser <[email protected]> >>>> Subject: Re: [HCP-Users] Skyra - BOLD and diffusion MRI protocols >>>> >>>> Hi Matt, >>>> >>>> 32 channel head coil. >>>> >>>> I was able to run the diffusion sequence on a phantom when TR/TE was >>>> 7000/106 ms. Since the scan time with this tr is already 20 minutes, I was >>>> thinking to acquire just b0 with PA phase encoding and the other 64 >>>> directions 2b data+b0 with AP. will that be okay? my concern is snr at te >>>> will not be very good and data may not be too great and may be atleast 2 >>>> reps are desired? >>>> >>>> Thanks >>>> >>>> Regards >>>> >>>> -VM >>>> >>>> On Dec 6, 2016 6:46 PM, "Glasser, Matthew" <[email protected]> wrote: >>>> >>>>> What coil are you using? >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> From: <[email protected]> on behalf of neuroimage >>>>> analyst <[email protected]> >>>>> Date: Tuesday, December 6, 2016 at 11:56 AM >>>>> To: "[email protected]" <[email protected]> >>>>> Subject: [HCP-Users] Skyra - BOLD and diffusion MRI protocols >>>>> >>>>> Hi, HCP Users and Developers. >>>>> >>>>> We have been trying to build a protocol for BOLD and DWI on our Skyra >>>>> (VE11C) using the latest release of HCP pulse sequences. But we >>>>> haven't been completely successful with what we wanted to achieve. >>>>> >>>>> A) BOLD: We were hoping to get a TR in the range of 750ms, res = 2mm3, >>>>> echo spacing (ES) approx 0.65. We were able to get to echo spacing of 0.69 >>>>> and all the other parameters with MB = 8. However, the sequence doesn't >>>>> run >>>>> and it gives us "Max amplitude overflow on gradient z axis" after MB >>>>> factor >>>>> exceeds 2. It appears to me that then we have to sacrifice TR and only >>>>> run >>>>> with MB = 2. Is there anybody with a Skyra who has able to achieve what we >>>>> are hoping for and willing to share the protocol with us? OR if somebody >>>>> could guide us to resolve the error of amplitude overflow. >>>>> >>>>> B) DWI: The idea was to have res = 1.5mm3, 2b-values at 1000 and 2500, >>>>> 64 directions with the best BW and ES achievable. The sequence runs for 7 >>>>> minutes out of total 13 minutes and gives gradient power amplifier error. >>>>> On Michael Harms's suggestion, I adjusted flip angle to 78/160 at a TR of >>>>> 5500 ms with excite/refocus pulse duration of 3840 and 7680. there was a >>>>> pop up warning that RF is clipped and the maximum refocusing angle was 142 >>>>> instead of 160. I placed a 64 directions diffusion vector and ran the >>>>> sequence under "free" mode. Again, I will appreciate if there is anybody >>>>> with a Skyra who has able to achieve what we are hoping for and willing to >>>>> share the protocol with us, along with the diffusion vector sets? OR if >>>>> somebody could guide us to resolve the error. >>>>> >>>>> Thank you. >>>>> >>>>> Regards >>>>> >>>>> --VM >>>>> >>>>> _______________________________________________ >>>>> HCP-Users mailing list >>>>> [email protected] >>>>> 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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If you have received this email >>>> in error, please immediately notify the sender via telephone or return >>>> mail. >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> [email protected] >>>> 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. If you have received this email >>> in error, please immediately notify the sender via telephone or return mail. >>> >> >> >> ------------------------------ >> >> 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. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > > > ------------------------------ > > 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. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
