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 63110 Email: [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. 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 >> >> >> ------------------------------ >> >> 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 >> > > > ------------------------------ > > 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
