Actually, have a look at this paragraph from the HCP rfMRI paper (http://www.sciencedirect.com/science/article/pii/S1053811913005338):
Echo-time (TE) was, after much discussion and evaluation, set to 33 ms. Again, this choice is a trade-off; long TE increases BOLD contrast, but decreases overall signal level and increases signal dropout in areas of B0 inhomogeneity. The TE for optimal functional CNR is equal to T2* when thermal noise dominates; however, T2* varies spatially, meaning that no single TE can be optimal throughout the entire brain. Acquiring multiple echoes in a single EPI readout train, or in separate acquisitions with multiple TEs, was not acceptable due to significantly prolonged readout duration and/or TR. Thus, the shortest TE that could be achieved without the use of partial Fourier or in-plane accelerations was selected, to minimise signal dropout. At 2 mm resolution, with the Connectome scanner gradients, this TE was 33 ms, given the excitation pulse width (~ 7 ms) required to achieve the (Ernst) flip angle (52°) for multiband x8. The use of partial Fourier to reduce TE resulted in larger signal dropouts than acquiring a full Fourier coverage of k-space with longer TEs (likely caused by local phase ramps in regions of B0 inhomogeneity shifting signal outside the acquired k-space region); hence partial Fourier was not utilised. The EPI echo train length is 52.2 ms for the final HCP fMRI protocol. The additional blurring along the phase encode direction due to apparent transverse relaxation (T2* ≈ 45 ms) in grey and white matter (Wansapura et al., 1999<http://www.sciencedirect.com/science/article/pii/S1053811913005338#bb0315>) in the final HCP fMRI protocol is generally not significant,4<http://www.sciencedirect.com/science/article/pii/S1053811913005338#fn0020> except in regions where the T2* is much shorter than the average. We carried out limited piloting to test whether adding small amounts (b ≈ 50s/mm2) of isotropic diffusion weighting (Boxerman et al., 1995; Wong et al., 1995<http://www.sciencedirect.com/science/article/pii/S1053811913005338#bb0020>) might reduce contributions from larger draining veins, but the improvements were not significant enough to warrant a longer consequential TE and subsequent reduction in SNR. The Prisma is not quite as capable as the HCP’s custom scanner, so TE=37 not 33. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Tuesday, August 1, 2017 at 8:23 PM To: HMZ <hmz...@163.com<mailto:hmz...@163.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Questions about parameters in CCF protocols 1. TI=1000 actually separates the CSF/Grey/White peaks of the the histogram more evenly than TI=900ms (CSF and Grey too close) or TI=1100 (Grey and White too close). I don’t understand why the FreeSurfer group has recommended TI=1100 as it wouldn’t seem to make things easier for their software. 2. I don’t remember the rational for the BOLD TE decision, but perhaps someone else does. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of HMZ <hmz...@163.com<mailto:hmz...@163.com>> Date: Tuesday, August 1, 2017 at 8:05 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Questions about parameters in CCF protocols Dear HCP team, This is Meizhen Han at Center for MRI research in Peking University. I read CCF protocol carefully and have 2 questions in my mind. I would be very appreciate it if you could share some ideas with me. 1/ Why the TI in T1w was changed from 1060ms(LS in UMN/CMRR) to 1000ms(CCF)? Is there some significant difference between them? I find that TI can influence the contrast, and the TI recommended by freesurfer group is 1100ms, and the TI in HCP main project is 1000ms. From your experience, do you think TI=1000ms is better? 2/ TE in BOLD sequence(in CCF) is 37ms, while in common BOLD protocols TE is 30ms usually. I think the echo should come at 30ms, and will decay significantly at 37ms. In my opinion, losing the edge of the k-space will blur the image and reduce SNR slightly. So why you choose TE = 37ms without a 7/8 partial fourier to shorten it? I have tested similar protocol, and I find if I choose a 7/8 partial fourier, the TE can be around 30ms. Any information and idea would help a lot! Looking forward to your reply. Thank you very much! Best wishes! -- Meizhen Han PhD Candidate Center for MRI Research Peking University Beijing, China _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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
