It is better for finding brain areas, but that bias correction will also remove low spatial frequency differences across subjects that you might be interested in (see Glasser et al 2013 Neuroimage for how it works).
The protocol looks fine, though TI=1000 would be better from the perspective of evenly spacing CSF, grey matter, and white matter tissue peaks in the image intensity histogram. Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Friday, July 14, 2017 at 2:34 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Calculation of myelin maps I'm using Myelin_BC as I thought it would be more accurate due to bias correction. I will recalculate with the normal myelin maps. Can you please tell me why MyelinMaps are better for the stats than MyelinMaps_BC? And do I understand correctly that our acquisition protocol is okay? Thanks a lot! On 14 July 2017 at 02:52, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Are you using Myelin or MyelinMap_BC? For finding brain areas use Myelin_BC, for statistics on the myelin itself you will want to use MyelinMap. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Thursday, July 13, 2017 at 7:25 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Calculation of myelin maps (just a correction: flip angle 9°, not 90 for MPRAGE) On 13 July 2017 at 12:19, Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote: Dear Matt, I completed all three structural pipelines and performed PALM comparison for myelin maps. However, the result I got was somewhat opposed to expectations (patients with early MS having significantly stronger myelination compared to healthy controls). I wondered that maybe something in our acquisition technique could have caused an error in the calculation (as they are a bit different from the HCP protocol)? I used the following images: 3D MPRAGE (TR = 1900 ms, TE = 2.55 ms, TI = 900 ms, flip angle = 90 , FOV = 240 x 240 mm2 , matrix size = 240 x 240, 176 slices, slice thickness = 1 mm), no fat suppression T2 SPACE (same matrix, FOV, and number of slices as in the T1w, TR=5000ms, TE= 393ms, flip angle = 120, slice thickness = 1mm), no fat suppression Is there anything that would have cause imprecise calculation of myelin maps or is it just how our results are? Thanks a lot!! Lisa _______________________________________________ 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
