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 <mha...@wustl.edu> 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 63110 Email: mha...@wustl.edu > > From: neuroimage analyst <neuroimage.anal...@gmail.com> > Date: Wednesday, December 7, 2016 at 1:54 PM > To: Michael Harms <mha...@wustl.edu> > Cc: "Glasser, Matthew" <glass...@wustl.edu>, " > hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > 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 <mha...@wustl.edu> 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: mha...@wustl.edu >> >> From: neuroimage analyst <neuroimage.anal...@gmail.com> >> Date: Wednesday, December 7, 2016 at 1:03 PM >> To: Michael Harms <mha...@wustl.edu> >> Cc: "Glasser, Matthew" <glass...@wustl.edu>, " >> hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> 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 <mha...@wustl.edu> 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: mha...@wustl.edu >>> >>> From: <hcp-users-boun...@humanconnectome.org> on behalf of "Glasser, >>> Matthew" <glass...@wustl.edu> >>> Date: Wednesday, December 7, 2016 at 11:49 AM >>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> Subject: [HCP-Users] FW: Skyra - BOLD and diffusion MRI protocols >>> >>> >>> >>> From: Matt Glasser <glass...@wustl.edu> >>> Date: Wednesday, December 7, 2016 at 10:14 AM >>> To: neuroimage analyst <neuroimage.anal...@gmail.com> >>> 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 <neuroimage.anal...@gmail.com> >>> Date: Tuesday, December 6, 2016 at 8:54 PM >>> To: Matt Glasser <glass...@wustl.edu> >>> 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" <glass...@wustl.edu> wrote: >>> >>>> What coil are you using? >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of neuroimage >>>> analyst <neuroimage.anal...@gmail.com> >>>> Date: Tuesday, December 6, 2016 at 11:56 AM >>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>> 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 >>>> 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. 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 >>> 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. If you have received this email >>> in error, please immediately notify the sender via telephone or return mail. >>> >>> _______________________________________________ >>> 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. 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. 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