[Freesurfer] TMI(total motion index) of diffusion MRI

Hello I’m attempting to analysis diffusion MRI using TRACULA. As mentioned on article "Spurious group differences due to head motion in a diffusion MRI study", I tried to calculate TMI(total motion index) first. The problem is that, upper and lower quartile of Percent Bad Slices are both 0.

[Freesurfer] Interpretting Brain Segmentation Volume to eTIV ratio

Dear FreeSurfer community, I wanted to interpret the BrainSegVol.to.eTIV ratio that is outputted from FreeSurfer version 5.2.0. In my sample of normally developing adolescents of ages 8 to 21, this ratio is between 0.65 and 0.85 for 98% of subjects. However, the value is less than 0.65 for 2%

[Freesurfer] group interaction with one continuous covariate and three nuisance variables (two continuous, one dichotomous)

Dear FS experts,I would like to test if the correlations between thickness/area and cognition differ between two groups, while age, socioeconomic status (continuous) and gender (dichotomous) should be nuisance variables.To look at the effect of cognition in one group only, I made a model with 8

[Freesurfer] controlling for Sex in a model using two continuous variables onto CTh

Dear FreeSurfer experts, We have run a vertex-wise analysis regressing a continuous variable onto cortical thickness on the surface, and would like to verify that our contrast that uses Age and Sex as covariates was defined correctly, especially since there is probably more than one way to

[Freesurfer] Call for Nominations - OHBM Student and Postdoc Special Interest Group {Disarmed} {Disarmed}

*Call for Nominations - OHBM Student and Postdoc Special Interest Group * Dear OHBM Members, The OHBM Student and Postdoc Special Interest Group (SIG) are seeking nominations for our 2017-2018 committee. The SIG provides a community of shared interests for OHBM trainees. The committee aims to

[Freesurfer] Multi-Subject Comparison in FreeSurfer

I am a new grad student and have been assigned a project in our Brain Imaging Research Center. I would be taking the time to push through and find these answers on my own but our program gives us 5 weeks of half days in a lab for a trial. So I am in a bit of a time crunch. I have been given

[Freesurfer] Cortical thickness map

Hello, Okay, thanks for the explanation. Is that thickness referring to the cortical thickness? Eva -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 29 August 2017 15:40 To: Freesurfer

Re: [Freesurfer] Cortical Thickness of Hippocampus subfields

Hi Vasudev, We don't have a direct way to measure the subfield thickness. We have tried a volumetric method to compute the thickness from the subfield masks though (http://nmr.mgh.harvard.edu/~koen/IglesiasNI2014.pdf , the "Experimental setup" section). It requires an isotropic-voxel soft

[Freesurfer] Centos 7 - hippocampal subfield segmentation in freeview

Dear freesurfer experts, after an update of my computer I finally use Centos 7 now. It seems as if some parts of the lateral hippocampal subfield segmentation are not visualized any more when using freesurfer. When using FSL, everything looks fine, though. Do you have any suggestions, what to

Re: [Freesurfer] Cortical thickness map

thickness isn't a surface - it's a scalar overlay over the surface. Try something like: freeview -f lh.inflated:overlay=lh.thickness with the appropriate paths to the surfaces and thickness files cheers Bruce On Tue, 29 Aug 2017, Esteban, Eva(GE Healthcare) wrote: Hello everyone,   I

[Freesurfer] sub-cortical analysis

Hi Dr Greve, I am using pet surfer to analyze suv images. I followed all the steps in wiki, I used the option mgx then I fed the images mgx.{ctxgm,subctxgm,gm} into surface based analysis for left and right hemispheres. I want to inquire about the sub cortical analysis. 1. I assume the

[Freesurfer] Cortical thickness map

Hello everyone, I am trying to overlay a cortical thickness map onto a subject but when I try this command freeview -v good_output/mri/T1.mgz good_output/mri/wm.mgz good_output/mri/brainmask.mgz good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 -f

[Freesurfer] mris_anatomical_stats error: missing ", " in "Measure Cortex, CortexVol Total cortical gray matter volume, ..."

Hi! It seems that in FreeSurfer 6, the comma between “CortexVol” and “Total cortical gray matter volume” is missing here’s the relevant part of one of my stats-files: # Table of FreeSurfer cortical parcellation anatomical statistics # # CreationTime 2017/08/23-20:19:44-GMT #

[Freesurfer] Freesurfer tutorial

Hi, That worked, thank you! From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: 22 August 2017 17:33 To: freesurfer@nmr.mgh.harvard.edu Subject: EXT: Re: [Freesurfer] Freesurfer tutorial try it without doing any

[Freesurfer] Error while running recon-all

Hello guys, I am trying to run recon-all command, i am getting the following error: error while loading shared libraries: libgomp.so.1: cannot open shared object file: No such file or directory Can anyone help me out with this. Thanks, Ritesh Mahajan