[Freesurfer] cluster feature extraction from qdec output

Dear experts, I would like to know what is the best and simplest way to extract cortical surface area and thickness from clusters obtained after a Monte Carlo correction. This is a group comparison I did with qdec including gender as discrete variable + age and mean thickness or whole hemispher

[Freesurfer] REPOST cluster feature extraction from qdec output

this… Thank you and best, Damien Damien MARIE Post-doctoral Fellow damien.ma...@unige.ch +41 22 379 08 49 - Brain and Language Lab Department of Clinical Neuroscience Biotech Campus 9 Chemin des Mines 1202

Re: [Freesurfer] REPOST cluster feature extraction from qdec output

order of subjects is first group “ dys “ then second group “ ct “ and that the contrast is called: rh-Diff-dys-dyslexic-control-intercept-area , negative p value means decrease of surface area in the first group (dys) as compared to the second group (ct), right ? Thank you and best, Damien

[Freesurfer] Processing 7T data

Dear experts, I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim is to look a R1 maps. I was wondering what was your opinion concerning the downsampling to 1 mm^3 (performed by the current FreeSurfer version if I am correct). What do you think would be the best: FreeSur

Re: [Freesurfer] Processing 7T data

> Best, > Falk > > -Ursprüngliche Nachricht- > Von: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Damien MARIE > Gesendet: Donnerstag, 6. Oktober 2016 14:01 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: [Freesurfer]

[Freesurfer] FreeSurfer 6 beta and mac osx el capitan

Hi, I would like to install the FreeSurfer 6 beta on my macbook pro (OS X El capitan 10.11.6, XQuartz 2.7.9 installed). I allowed applications downloaded from Anywhere in privacy and settings, and disabled csrutil (the System Integrity Protection, a security feature that hobbles some of the ca

Re: [Freesurfer] FreeSurfer 6 beta and mac osx el capitan

Hi, I downloaded the archive with Firefox instead of Safari and problem is solved. Strangely, the archive downloaded with Safari was not full. Damien > On 10 Oct 2016, at 16:56, Damien MARIE wrote: > > Hi, > > I would like to install the FreeSurfer 6 beta on my macbo

Re: [Freesurfer] Quantifying volumes

Hi, Just adding a word about the e-mail of ma colleague Josue. What he meant is that he extracted volumes for exactly the same ROI (a merging of destrieux labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using 1- a .curv file of this ROI, mri_binarize and mri_segstats or 2- a .la

[Freesurfer] Sulcal depth variations

Hello everyone, I'm working on a group analysis of cortical thickness, surface area, curvature and sulcal depth with FreeSurfer 5.3. However I'm in trouble concerning the interpretation or the meaning of my results, especially concerning curvature and sulcal depth. I understood that curvature

[Freesurfer] ERROR

Hi, I ran recon-all on a server where Ubuntu is running. Recently I installed separately freesurfer on a macbook, it is working (e.g. tkmedit bert), I moved my processed subjects to freesurfer/subjects on the macbook but I can not work with them. I have the below error. I changed the permissio

[Freesurfer] ERROR

an issue with mac os (10.11.6 ?) and copy pasting files in a subdirectory of the Applications folder… Thanks, Damien ___ Damien MARIE <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Damien+MARIE%22> Sat, 15 A

[Freesurfer] Any advices for hires surface reconstruction?

Hi, I have a project on 7T data. I processed 26 subjects with FreeSurfer6 recon-all with or without the hires flag. The input is MP2RAGE, 0.6 mm^3, bias corrected, skull strip was done despite a slight piece of dura is still present. For the data processed at native resolution, with the hires f

Re: [Freesurfer] Any advices for hires surface reconstruction?

oug On 4/17/17 1:45 PM, Damien MARIE wrote: Hi, I have a project on 7T data. I processed 26 subjects with FreeSurfer6 recon-all with or without the hires flag. The input is MP2RAGE, 0.6 mm^3, bias corrected, skull strip was done despite a slight piece of dura is still present. For the data

[Freesurfer] mri_mcsim update and FreeSurfer6

ME/bin/mri_mcsim “ here: https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo <https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo> I am working with FreeSurfer6, should I update it or it was implemented in the version 6? Thank you and best,

[Freesurfer] Looking for advices on the best parameters to use with a Montecarlo cluster-wise correction

Hi, I would like to get your opinion about Montecarlo statistics. I know that there is maybe not a simple answer and that it depends probably on the research question but anyway, is there some kind of gold standard about the number of montecarlo simulations / p values ? Speaking about that wit

[Freesurfer] mean hemispheric value in a .mgh

Hi, I’ve a .mgh that is a volume projected on the surface of the same subject at mid-thickness (output of mri_vol2surf) . I would like to extract the mean hemipheric value in this X.mgh. I guess it is possible with mris_anatomical stats but probably my command line is incorrect (see below). A

[Freesurfer] Average hemispheric R1 value

Dear experts, I would like to extract the mean left / right R1 value for each of my subjects (R1 = 1/T1). I did that with mris_anatomical_stats (see below) and I’m assuming that “ average cortical thickness = 0.001 mm +- 0.000 mm “ is my average R1 value (in that case for the right hemi). Is th

[Freesurfer] glm results : opposite direction between whole-brain analysis and feature extraction in the significant clusters

Hi, I am working on R1 maps. I ran a very simple glm on smoothed R1 maps, FWHM = 8 mm, population 1, population 2 , and age as nuisance factor. After POS MC simulation CW correction, I had two significant clusters resulting from this in the planum temporale and Heschl’s sulcus. The contrast bei

[Freesurfer] Myelinated cortical thickness ratio map

External Email - Use Caution Dear experts, I am working with R1 maps that I project on the surface. The goal is to look at intra-cortical myelin. I detect interesting effects between two groups. Now I would like to compute myelinated cortical thickness ratio maps, in order to c

Re: [Freesurfer] Myelinated cortical thickness ratio map

t;http://nmr.mgh.harvard.edu/><mailto:freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>> > on behalf of Damien MARIE http://damien.ma/>...@unige.ch > <http://unige.ch/><mailto:damien.ma...@unige.ch > <mailto:damie

[Freesurfer] myelin and thickness pvr

External Email - Use Caution Dear freesurfer experts, I would like to replicate an analysis I did with qdec but regressing out thickness at the vertex level. It’s a myelin group contrast with age and left average myelin as nuisance factors. I used the mri_glmfit command line ge

[Freesurfer] myelin group difference and pvr of thickness

External Email - Use Caution Hi, I would like to replicate an analysis I did with qdec but regressing out thickness at the vertex level. It’s a myelin group difference with age and left average myelin as nuisance factors. Q1/ should I use smoothed thickness maps or unsmoothed?

[Freesurfer] myelin analysis with cortical thickness pvr

External Email - Use Caution Hi, I would like to replicate an analysis I did with qdec but regressing out thickness at the vertex level. It’s a myelin group difference with age and left average myelin as nuisance factors. I used the mri_glmfit command line generated during that