Ah, I didn't realize that you were referring to that in the 3rd paragraph. thanks.
-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 3:23 PM, Glasser, Matthew <[email protected]> wrote: > -cifti-correlation-gradient does a second order correlation (where you > had used eta^2), taking a .dconn.nii as its input. The first order > correlation is done with -cifti-correlation from a .dtseries.nii to a > .dconn.nii. > > I already explained about click view maps for .dconn.nii. ;) > > Peace, > > Matt. > > From: Alex Cohen <[email protected]> > Reply-To: "[email protected]" <[email protected]> > Date: Wednesday, April 22, 2015 at 3:19 PM > To: Matt Glasser <[email protected]> > Cc: "[email protected]" <[email protected]> > Subject: Re: [HCP-Users] cifti-correlation-gradient settings and > surface-based math? > > 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. 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