Interesting, thanks for the numbers. I am using FEAT and ICA+FIX as my preprocessing as well, so that should be less of an issue.
Of note, my impression from the wb_command help was that correlation-gradient was doing BOTH correlation and gradient->average... wrapped up into one tool. is this not correct and one needs to run cifti-correlation prior??? (also, any idea regarding the click-view of correlation maps? Donna?) -Alex ---------------------------------------------------------------- *Alexander Li Cohen, M.D., Ph.D.* Resident Physician Child and Adolescent Neurology E-mail: [email protected] (Medical/Science Email) E-mail: [email protected] (Lifetime Email) *Mayo Clinic* 200 First Street SW Rochester, MN 55905 mayoclinic.org ---------------------------------------------------------------- On Wed, Apr 22, 2015 at 2:45 PM, Glasser, Matthew <[email protected]> wrote: > Hi Alex, > > For group data I usually use a gradient pre-smoothing of 1mm sigma, > though for some modalities like myelin maps, even this reduces some detail > (you might try both ways…). For seed exclusion I use 2mm (the acquisition > resolution), basically the goal is to exclude the central spike in > correlation. Recently we’ve found that the fisher z transform distorts > gradients some (relative to other modalities) and global signal > regression/MGTR distorts them more (basically moving gradients towards > cortical areas that are more correlated with the global sensory systems > signal). This is one of the reasons we’ve stopped doing global signal > regression/MGTR, though there remains debate on this issue in some quarters > of the HCP. To avoid using things like global signal regression, use of a > denoising approach like ICA+FIX is absolutely critical (and is important > anyway, as past approaches to denoising did not address spatially specific > temporal artifacts in a data driven way, possibly leading to things like > distance dependent artifacts that are possibly then exacerbated by using > global signal regression). > > There is also a difference of opinion on edge detection and we don’t use > it (preferring to stay closer to the original data and avoid thresholding), > though others do. We have not implemented edge detection in Connectome > Workbench, but I believe someone has code that uses wb_command outputs and > computes this in matlab. > > This is how you visualize CIFTI dense connectomes .dconn.nii, and so > this is a core feature of Connectome Workbench. Note that one uses > -cifti-correlation to compute the dense connectome and then > -cifti-correlation-gradient to compute the gradients. > > Peace, > > Matt. > > From: Alex Cohen <[email protected]> > Reply-To: "[email protected]" <[email protected]> > Date: Wednesday, April 22, 2015 at 2:19 PM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] cifti-correlation-gradient settings and > surface-based math? > > Hi all, > Two quick (ok three) fcMRI questions: > > - What settings have you all been using for calculating surface-based > gradients with resting BOLD data for surface presmoothing, seed exclusion > and the like? > > - Is there a a list of methods using wb_command for doing surface-based > image processing beyond simple gradient (e.g., like edge detection, etc...) > I know there is extrema detection, but just wondering what else is > available... and/or how to implement things like this... > > - As a side-note, back in the Caret days there was a function where you > could click on the surface and the associated correlation map would appear > on the surface (assuming it was already made)... Did this make it into > wb_view? and/or was adapted for CIFTI files containing correlation maps? > > -Alex > > ---------------------------------------------------------------- > *Alexander Li Cohen, M.D., Ph.D.* > Resident Physician > Child and Adolescent Neurology > E-mail: [email protected] (Medical/Science Email) > E-mail: [email protected] (Lifetime Email) > > *Mayo Clinic* > 200 First Street SW > Rochester, MN 55905 > mayoclinic.org > ---------------------------------------------------------------- > > _______________________________________________ > HCP-Users mailing list > [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
