Hi, It turned out that minimum echo spacing required for 2mm3 BOLD data was 0.75ms with partial fourier 7/8. I was always trying for minimum achievable and that was a mistake. So, for now all works , atleast on the phantom.
Thanks for all your help and suggestions! Regards --VM On Thu, Dec 8, 2016 at 2:08 PM, Harms, Michael <[email protected]> wrote: > > The CMRR MB website has example DICOMs from BOLD that you could try > importing onto your Skyra. > > Also, if you running VD13, you could try importing an .exar1 protocol file > for VD13 that we have hosted here: > http://protocols.humanconnectome.org/CCF/ > > 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: [email protected] > > From: "Glasser, Matthew" <[email protected]> > Date: Thursday, December 8, 2016 at 3:58 PM > To: neuroimage analyst <[email protected]> > Cc: Michael Harms <[email protected]>, "[email protected]" < > [email protected]> > > Subject: Re: [HCP-Users] FW: Skyra - BOLD and diffusion MRI protocols > > The issues hitting the target BOLD resolution are quite puzzling, I would > ask the U Minn folks to see if they know what is going on. > > Peace, > > Matt. > > From: neuroimage analyst <[email protected]> > Date: Thursday, December 8, 2016 at 4:56 PM > To: Matt Glasser <[email protected]> > Cc: "Harms, Michael" <[email protected]>, "[email protected]" < > [email protected]> > Subject: Re: [HCP-Users] FW: Skyra - BOLD and diffusion MRI protocols > > 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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