Re: [Freesurfer] questions about split region from the 7 and 17 networks, from huasheng liu

Hi Huasheng, Here you go: https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_SplitLabels.zip I am also cc-ing the freesurfer list. --Thomas On Tue, Aug 30, 2016 at 11:05 AM, liuhas_20040125 wrote: > Dear professor Yeo : > > > > My name is

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

Hi, I wouldn’t say that non-orthogonal designs are “wrong” to use with permutation. Rather, there are different approaches to handling that situation and produce approximate p-values. See Table 2 in Winkler’s 2014 paper, and the results therein comparing the various approaches:

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

PALM handles GIFTI and CIFTI data. Peace, Matt. On 8/29/16, 6:21 PM, "Douglas N Greve" wrote: >Does PALM do surface-based? Also, there is no way to appropriately >handle this. For permutation, non-orthogonal

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

Does PALM do surface-based? Also, there is no way to appropriately handle this. For permutation, non-orthogonal designs are wrong. There are ways to try to compensate for it, which is what PALM is doing. Sorry to be nit-picky! On 08/29/2016 06:12 PM, Harms, Michael wrote: > Hi Maaike, > Why

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

Hi Maaike, Why not just use PALM? Then you don’t have to worry about this (since PALM appropriately handles the situation of correlated covariates). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

It is hard to say. Since the subjects are not exchangeable, the permutation is technically not appropriate. Check the winkler paper, I think he talks about what happens if you just don't do anything. On 08/29/2016 11:07 AM, maaike rive wrote: > > Hi all, > > > Is using forced permutation for

Re: [Freesurfer] Reproducibility of freesurfer analyses across different version of linux

On 29 August 2016 at 02:24, Knut J Bjuland wrote: > Is it possible to use a script to extract information about which library > that is used for each recons?Or are there any other means to get this > information? I'm not sure about that. At least some of the info is

Re: [Freesurfer] Results different between mean-centered and raw covariates -- glm_fit

You definitely do not want to demean within group. Having said that, no demeaning method is more "sound" than the other. The problem is in the interpretation. Imagaine you have a plot of volume vs ICV for each group. When you have an interaction, the best-fit lines will intersect at some ICV.

Re: [Freesurfer] Results different between mean-centered and raw covariates -- glm_fit

Yes, I agree completely. We are using DODS and it is clear that we have different results depending on which type of ICV we use. The question is... which type of ICV correction for DODS is the most statistically sound? demean across all groups, no demeaning, or demean within groups separately.

Re: [Freesurfer] Results different between mean-centered and raw covariates -- glm_fit

If there was not an interaction between group and ICV, I would say to use DOSS where demeaning does not make a difference. Since there is an interaction, you have to use DODS, but the interpretation is no longer easy. If you do not demean, then you are implictly testing for a difference at

Re: [Freesurfer] Results different between mean-centered and raw covariates -- glm_fit

Sorry for not specifying. Yes, we are looking at difference in volume between the two groups using DODS. What is the most statistically sound... raw values, demeaning across the entire sample, or demeaning with groups separately? FYI, I exported the ICV values to SAS and there is a significant

Re: [Freesurfer] Results different between mean-centered and raw covariates -- glm_fit

not sure what you are testing, but if you are, eg, looking at the difference between two groups regressing out ICV, then it can make a huge difference On 08/29/2016 12:36 PM, Corinna Bauer wrote: > Hello all, > > I am wondering why results would change completely for between group > volume

Re: [Freesurfer] volume, surface area, and thickness

Hi Woo-Suk why not just do the surface analysis that they are requesting? I'm not sure what you are asking, but certainly volume = surface area * thickness in general, and so a volumetric effect can be driven by one or both of surface area and thickness cheers Bruce On Sat, 27 Aug 2016,

Re: [Freesurfer] wm.mgz enclosed in pial/white surface

do you mean the ones that are between the two surfaces? You could use mris_fill to fill the interior of the white then use it as a mask in mri_mask cheers Bruce On Sun, 28 Aug 2016, Fire Tech wrote: Dear all   I am searching for a solution to remove wm.mgz voxels which are enclosed by

[Freesurfer] Results different between mean-centered and raw covariates -- glm_fit

Hello all, I am wondering why results would change completely for between group volume analysis when using demeaned/mean-centered ICV compared to using ICV as a covariate in mri_glmfit? See the figures below. Does demeaning the covariate inherently change the results comapred to the raw

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

Hi all, Is using forced permutation for non-orthogonal design matrices wrong or is it allowed to do this instead of using tools like palm (what happens eg with the covariates when using forced permutation)? I used forced permutation and it seemed to work, results were (partly) comparable to

[Freesurfer] How to transfer the VTK cortical surface to the diffusion space?

Hi there! Since this is my first time using FreeSurfer, I found it quite challenging to get the handle on the different coordinate systems used. My goal is to generate vtk files where the vtk cortical surface and the vtk fiber tracts are in the same space (for one individual subject). Basically,

Re: [Freesurfer] Reproducibility of freesurfer analyses across different version of linux

On 08/28/2016 05:57 PM, R Edgar wrote: On 28 August 2016 at 06:59, Knut J Bjuland wrote: I found this paper about named “Reproducibility of neuroimaging analyses across operating systems” (Glatard et al., 2015). There were differences in cortical morphometry like