[Freesurfer] ICV adjustment of volumes in longitudinal pipeline

External Email - Use Caution Hello Freesurfer experts, If I want to analyze the volume difference of regions (2 time points) after performing all the 3 steps of the longitudinal pipeline, do I need to adjust each volume in the "long" directories to its specific "tp.long" ICV or ar

[Freesurfer] Job offer - 2 year postdoc France

External Email - Use Caution Applications are invited for a two year, full time postdoctoral position (see below for details). Contact Dr. Martine Migaud (martine.mig...@inra.fr) for questions. Job title: Multi-modal MRI analysis of a large mammalian brain model Structure: A 2-

[Freesurfer] Longitudinal errors, Voxel size differs

External Email - Use Caution Hi FS Experts, I'm trying to run a longitudinal analysis across three timepoints and have run the cross steps for the data. I then ran the base step but found that my voxel dimensions are slightly different across the timepoints and I got the follow

Re: [Freesurfer] Pial surface running into white surface

Hi Dr. Kevin Aquino - could you please upload the entire subject directory? At first glance, it looks like fs is incorrectly including gm in the wm.mgz just superior to the surface errors you're seeing - the cluster of voxels w/ intensity 250 around the coordinate 87 178 97 in the wm.mgz. Try e

Re: [Freesurfer] pcc.nii.gz vs z.nii.gz resting state

Hi Lauri, the z we compute is based on the transform from a p-value, not the r-value. This is often referred to as a "pseudo-z". The pseudo-z depends on the degrees of freedom. Now that you mention it, it would probably be better to use the r-to-z transform to compute something closer to a real

Re: [Freesurfer] Contrast interpretation - between-groups mean

depends on what you are getting the direction of the result for and how you want to interpret it. If the cluster has both pos and neg, then the interpretation becomes more difficult. Is this really happening? I don't think I've ever seen it. The abs() just takes the absolute value, there is no

[Freesurfer] Neuroimaging postdoc position available at the University of Michigan

External Email - Use Caution *Research Fellow - Multimodal neuroimaging of Parkinson’s disease* A Research Fellow position is available immediately at the Functional Neuroimaging, Cognitive, and Mobility Laboratory, Department of Radiology, University of Michigan, Ann Arbor, MI, U

[Freesurfer] correlation analysis

External Email - Use Caution Dear Freesurfer team, I'm working on correlation between fMRI data and a clinical score. Since such fMRI data correlate also with cortical thickness, I'd like to regress out this variable (cortical thickness). How can I write my fsgd file and command

Re: [Freesurfer] correlation analysis

You have to use a per-vertex regressor (--pvr to mri_glmfit). Search through the mail archives to find instructions On 05/15/2018 03:53 PM, Raffaele Dubbioso wrote: > > > Dear Freesurfer team, > > I'm working on correlation between fMRI data and a clinical score. > Since such fMRI data correlat

Re: [Freesurfer] Problem with template longitudinal pipeline

Hi Laura, it could be that 9 years of severe aging or neundegenerative disease are too far apart for the method to cover the distance. The base would look blurry or show ghosting (in 2 time points the median is equal to the mean and the mean will not look good with too much change). I would re

Re: [Freesurfer] Longitudinal LME cluster value extraction

Hi Emmanuel, I think this should be identical to the cross sectional situation, you map that cluster (defined on FSAVERAGE) to each subject_time_point and then use mri_segstats to get stats on that region. Probably others can help you with what tools exactly you need for this (or probably this

Re: [Freesurfer] ICV adjustment of volumes in longitudinal pipeline

Hi Tamir, ICV is fixed across time (derived from the template image), so that data can be compared directly, but for cross subject analysis you still need to adjust for ICV of course. Best, Martin > On 15. May 2018, at 03:19, Tamir Eisenstein wrote: > > > > Hello Freesurfer experts, > >

Re: [Freesurfer] Longitudinal errors, Voxel size differs

Hi Erik, you should investigate why this is the case. Any difference in acquisition will cause effects and it will be impossible to distinguish these from real effects. Also you should never just resample one time point, as that will introduce processing bias. I would advise to - find out why