Yes. What was the TR and voxel size of the images you showed for which the ventricles were more prominent in the std maps? We don’t have much anatomical contrast in the BOLD at TR=720 ms. Plus at 2 mm resolution we are thermal noise dominated (so even if the ventricles have more “physiological noise” variation, it won’t be as evident).
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 St. Louis, MO 63110 Email: [email protected] From: <[email protected]<mailto:[email protected]>> on behalf of Stephen Smith <[email protected]<mailto:[email protected]>> Date: Tuesday, November 1, 2016 at 2:13 AM To: Chris Gorgolewski <[email protected]<mailto:[email protected]>> Cc: Hcp Users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Fluctuations of the CSF in the ventricles I suspect this simply comes down to the low TR resulting in suppressed CSF signal - not directly the use of multiband or a specific recon. Steve. On 31 Oct 2016, at 23:38, Chris Gorgolewski <[email protected]<mailto:[email protected]>> wrote: That's what the reference manual is suggesting as well, but it's not clear on what was used for fMRI (which the picture above is an example of). Best, Chris On Mon, Oct 31, 2016 at 4:35 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: I believe it is regular multi-band (SENSE=1 was used for diffusion, but not I think for fMRI). Peace, Matt. From: Chris Gorgolewski <[email protected]<mailto:[email protected]>> Date: Monday, October 31, 2016 at 6:33 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: Hcp Users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Fluctuations of the CSF in the ventricles So what reconstruction algorithm was used in HCP? Best, Chris On Mon, Oct 31, 2016 at 4:31 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: I wonder if this has to do with the TR used or the number of dummy scans deleted? We did not use GRAPPA for our functional data. Peace, Matt. From: Chris Gorgolewski <[email protected]<mailto:[email protected]>> Date: Monday, October 31, 2016 at 6:27 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: Hcp Users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Fluctuations of the CSF in the ventricles Here's an example of a standard deviation map of a single band scan clearly showing the ventricles: <image.png> It's not always very prominent, but you can usually see this in one form or another. Here's one more example (different site, scanner, sequence - still single band): <image.png> Here are some variance maps from multiband data we acquired on our GE scanner (left is the reconstructed with SENSE/GRAPPA right is reconstructed with split-slice grappa, bottom the difference): <image (1).png> I'm reaching out to the HCP community, because a) I also see the absence of the ventricular variance in the HCP data b) AFAIK the HCP data was also reconstructed with split-slice grappa. Have anyone noticed this before? Do you know what's the cause? Best, Chris On Mon, Oct 31, 2016 at 4:13 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: Could you provide an example of what you want it to look like? Peace, Matt. From: Chris Gorgolewski <[email protected]<mailto:[email protected]>> Date: Monday, October 31, 2016 at 6:11 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: Hcp Users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Fluctuations of the CSF in the ventricles Nope - this is raw. Not even gradient distortion corrected. Best, Chris On Mon, Oct 31, 2016 at 3:28 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: Is this cleaned data? Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Chris Gorgolewski <[email protected]<mailto:[email protected]>> Date: Monday, October 31, 2016 at 1:45 PM To: Hcp Users <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Fluctuations of the CSF in the ventricles Dear all, I've been evaluating different multiband reconstruction algorithms and I came across a weird property of one of them - lack of sensitivity to signal variance of the CSF in the ventricles. As a sanity check, I looked at the HCP data and it shows the same property. Here's an example (left: mean image; right: standard deviation) <image.png> In single band images and some multiband reconstructions, ventricles are prominent on standard deviation maps, yet they seem to be missing in HCP data. Does anyone know why is that? IS it a property of the multiband reconstruction used here? Best, Chris _______________________________________________ HCP-Users mailing list [email protected]<mailto:[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. 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. ________________________________ 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 [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [email protected]<mailto:[email protected]> http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet<http://smithinks.net> _______________________________________________ HCP-Users mailing list [email protected]<mailto:[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. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
