[Freesurfer] Error from Generating mean value for clusters that survived multiple comparison correction in QDEC

Dear FreeSurfer experts, Am working on this machine: *FREESURFER_HOME: /usr/local/freesurferBuild stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0Debian version: jessie/sidKernel info: Linux 3.19.0-28-generic x86_64* Am trying to extract the mean LGI value for a cluster from QDEC using m

[Freesurfer] Longitudinal single time point cross sectional comparison

Dear Freesurfer users, I have longitudinal data with three time points but want to run a cross sectional comparison on the first instance between group on just one time point (using QDEC). Any Idea on how I could do that on longitudinal data. Thanks for your help. Emmanuel Nwosu

[Freesurfer] Fwd:

Hi Am having a bit of a problem that may be easy to resolve. I want to view an LGI two-group comparison I did in mri glm-fit with freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mgh). The grayscale inflated surface turns red like what is in picture-1 Please have anyone an idea

[Freesurfer] grayscale display turns red in freeview

Hi Am having a bit of a problem that may be easy to resolve. I want to view an LGI two-group comparison I did in mri glm-fit with freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mgh). The grayscale inflated surface turns red like what is in picture-1 Please have anyone an idea

Re: [Freesurfer] grayscale display turns red in freeview

n Nov 21, 2016, at 3:52 AM, Emmanuel Nwosu > wrote: > > Hi > > Am having a bit of a problem that may be easy to resolve. > > I want to view an LGI two-group comparison I did in mri glm-fit with > freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mgh). >

Re: [Freesurfer] grayscale display turns red in freeview

it opens a blank "configure overlay" dialog, then the screen goes dark On Mon, Nov 21, 2016 at 4:29 PM, Ruopeng Wang wrote: > What happens when you click on the button? > > On Nov 21, 2016, at 9:02 AM, Emmanuel Nwosu > wrote: > > Thanks Ruopeng. I can't open

Re: [Freesurfer] grayscale display turns red in freeview

GUI. Run “freeview -h” and look for > surface overlay related options. > > On Nov 21, 2016, at 9:48 AM, Emmanuel Nwosu > wrote: > > Yes am running it on a remote server. Here is the screen shot > > On Mon, Nov 21, 2016 at 4:40 PM, Ruopeng Wang > wrote: > >> Can yo

[Freesurfer] correlation in mri glmfit controlling for 2 categorical variables and 1 continuous variable

Hi All Am not sure if I can do this in mri glmfit I want to investigate the relationship between cortical thickness and a continuous variable (A) while accounting for two categorical variables with two levels each and one continuous variable. That is I want to account for : 1. categorical variabl

[Freesurfer] Error in Qcache

Hi All, I will want to know if this error on this link https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051464.html was resolved. I am having a similar problem while sampling to the fsaverage. Thanks Kind regards Emmanuel ___ Freesurfer

[Freesurfer] extracting morphometric values from co-ordinates

Dear FreeSurfer Experts, Am wondering if there is a way to extract morphometry (cortical thickness, area, etc) values from a specific co-ordinate (talaraich, MNI, etc) of interest. Any help with this will be appreciated. Kind regards Emmanuel ___ Frees

Re: [Freesurfer] extracting morphometric values from co-ordinates

res like thickness though. > > cheers > Bruce > > > On Wed, 4 Apr 2018, Emmanuel > Nwosu wrote: > > > Dear FreeSurfer Experts, > > > > Am wondering if there is a way to extract morphometry (cortical > thickness, area, etc) values from a > > specific co-or

[Freesurfer] Longitudinal LME cluster value extraction

External Email - Use Caution Dear FreeSurfer experts, Am analysing longitudinal structural data with the LME model algorithm. I will like to map the significant cluster after analysing the data to all subjects at all time points, extract the values for all and perform further stat

[Freesurfer] mri_label2label: Empty label file

External Email - Use Caution Dear FreeSurfer users, I want to extract the thickness value of a significant cluster from all the subjects used for a comparison for further statistical analyses. I ran the mri_surfcluster first to create the ROI label with fsaverage and then used mr

[Freesurfer] lme_mass_F error

External Email - Use Caution Dear All I am running the longitudinal post processing statistical analysis and this error comes up each time I run the lme_mass_F. Does anyone have an idea of why this is happening and how to resolve it. Any help will be appreciated ***