Thank you. Regards -VM On Dec 9, 2016 1:01 PM, "Harms, Michael" <mha...@wustl.edu> wrote:
> > In terms of actually processing your data, I would use the actual b-values > reported by dcm2nii. In terms of reporting the “b-values” that you used in > a publication, people would just say “0, 1000, and 2500”. > > -- > 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: <hcp-users-boun...@humanconnectome.org> on behalf of neuroimage > analyst <neuroimage.anal...@gmail.com> > Date: Friday, December 9, 2016 at 2:49 PM > To: dgw <dgwake...@gmail.com> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] FW: Skyra - BOLD and diffusion MRI protocols > > Hi, all. > > > I ran one subject with dMRI data and I have attached the protocol and the > bvals as obtained from dcm2nii. As can be seen in the attached protocol > "diff_sequence.pdf" I only specify 3 b-values 0, 1000 and 2500 but as can > be seen from the bvals file there are 9 bvalues (5, 995, 1000, 1005, > 2490,2495,2500,2505,2510) I understand when I ask the scanner to play b0 it > doesnt really play b0 but close to 0 which is 5 in this case. Can i then > assume 5 to be close to b0, 995,1000,1005 to be 1000 and 2490-2510 to be > 2500 but when I write this for reporting purposes or any other processing > steps, I can say only 3 b-values at 0,1000, and 2500? > > I know I have done A>>P here but I will change it to P>>A following > dgwakeman's suggestion. > > Thanks > > Regards > > --VM > > > On Thu, Dec 8, 2016 at 6:59 PM, neuroimage analyst < > neuroimage.anal...@gmail.com> wrote: > >> Thank you for your suggestion. I will use that p>>a for subject test. >> >> Regards >> >> --VM >> >> On Thu, Dec 8, 2016 at 6:32 PM, dgw <dgwake...@gmail.com> wrote: >> >>> If you are only doing one phase encode direction, I would strongly >>> recommend doing p>a. It has a large number of advantages particularly in >>> the frontal lobes. >>> >>> hth >>> D >>> >>> Sent from my Phone >>> >>> On Dec 8, 2016, at 16:56, neuroimage analyst < >>> neuroimage.anal...@gmail.com> wrote: >>> >>> A>>P >>> >>> Thanks >>> >>> Regards >>> >>> --VM >>> >>> On Thu, Dec 8, 2016 at 1:40 PM, Glasser, Matthew <glass...@wustl.edu> >>> wrote: >>> >>>> What phase encoding directions are you using? >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: neuroimage analyst <neuroimage.anal...@gmail.com> >>>> Date: Thursday, December 8, 2016 at 1:37 PM >>>> To: "Harms, Michael" <mha...@wustl.edu> >>>> Cc: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org" >>>> <hcp-users@humanconnectome.org> >>>> 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 <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 63110Email: 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. 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 >>> >>> >> > _______________________________________________ > 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
