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 St. Louis, MO 63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of neuroimage analyst <neuroimage.anal...@gmail.com<mailto:neuroimage.anal...@gmail.com>> Date: Friday, December 9, 2016 at 2:49 PM To: dgw <dgwake...@gmail.com<mailto:dgwake...@gmail.com>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto: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<mailto:neuroimage.anal...@gmail.com>> wrote: A>>P Thanks Regards --VM On Thu, Dec 8, 2016 at 1:40 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: What phase encoding directions are you using? Peace, Matt. From: neuroimage analyst <neuroimage.anal...@gmail.com<mailto:neuroimage.anal...@gmail.com>> Date: Thursday, December 8, 2016 at 1:37 PM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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<tel:(314)%20747-6173> St. Louis, MO 63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: neuroimage analyst <neuroimage.anal...@gmail.com<mailto:neuroimage.anal...@gmail.com>> Date: Wednesday, December 7, 2016 at 1:54 PM To: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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<tel:(314)%20747-6173> St. Louis, MO 63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: neuroimage analyst <neuroimage.anal...@gmail.com<mailto:neuroimage.anal...@gmail.com>> Date: Wednesday, December 7, 2016 at 1:03 PM To: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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<tel:(314)%20747-6173> St. Louis, MO 63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Wednesday, December 7, 2016 at 11:49 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] FW: Skyra - BOLD and diffusion MRI protocols From: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Wednesday, December 7, 2016 at 10:14 AM To: neuroimage analyst <neuroimage.anal...@gmail.com<mailto: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<mailto:neuroimage.anal...@gmail.com>> Date: Tuesday, December 6, 2016 at 8:54 PM To: Matt Glasser <glass...@wustl.edu<mailto: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<mailto:glass...@wustl.edu>> wrote: What coil are you using? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of neuroimage analyst <neuroimage.anal...@gmail.com<mailto:neuroimage.anal...@gmail.com>> Date: Tuesday, December 6, 2016 at 11:56 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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. 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