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]> > 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 > <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] > 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] http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
