[Freesurfer] LME model and contrast

Dear freesurfer team, I’m trying to use freesurfer LME tools to check whether baseline BMI scores (BMI scores at the first timepoint) have a statistically significant effect/impact on longitudinal thickness changes accounting for baseline age and gender. The model I’m thinking of is: Y_ij =

Re: [Freesurfer] Why does nii2mnc fail with a neck-cropped-structural Image?

Hi, Writing this question helped me find my own mistake. I have been using output_better.nii.gz instead of output_better.nii. Running gunzip extraction before nii2mnc solves the problem. Thanks alot, Usman Ayub Sheikh On Thu, Sep 7, 2017 at 4:32 PM, Usman Ayub wrote: > Hi

[Freesurfer] combining a stroke lesion label with aseg.presurf.mgz

Hello FreeSurfer expert, I have a binarized stroke masks of 200 stroke patients that were hand traced. Since, we have a lot of patients, it will take a lot of time to edit the aseg.presurf.mgz. The stroke masks were drawn in the native space and I want to bring them into the freesurfer space, and

[Freesurfer] [TENURE-TRACK POSITION IN CLINICAL NEUROSCIENCE AT OHIO STATE UNIVERSITY]

[POSTED ON BEHALF OF RUCHIKA PRAKASH] Dear Colleagues: The Department of Psychology at Ohio State University is looking to hire a tenure-track assistant professor in the area of clinical neuropsychology/neuroscience. We are specifically looking for candidates with the potential to establish a

[Freesurfer] Cluster-Defining Threshold of p=0.025

Hello, Is it possible to use cluster-defining thresholds such as p = 0.025 with mri_glmfit-sim? (This would roughly correspond to a negative log value of 1.6.) My design doesn't allow the use of permutations for simulating cluster sizes, so I have to use the mczsim option; however, from what I

[Freesurfer] Why does nii2mnc fail with a neck-cropped-structural Image?

Hi Freesurfer People, The aim is get ROI masks for my functional images and to achieve that for each of the subjects in my data, I am: 1. Running freesurfer for segmentation of structural scan, 2. Running feat analysis that would give me transformation matrices including structural2functional

Re: [Freesurfer] combining a stroke lesion label with aseg.presurf.mgz

Thanks doug. If I run the recon-all -autorecon2-noaseg -autorecon3. Will it incorporate the stroke? Also, does it matter if it's a cortical stroke and i am using v6.0 and i don't see aseg.manedit.mgz. Best, Paul On Thu, Sep 7, 2017 at 12:38 PM, Douglas N Greve wrote:

Re: [Freesurfer] combining a stroke lesion label with aseg.presurf.mgz

try something like mergeseg --src aseg.presurf.mgz --merge stroke.mgz --o aseg.manedit.mgz --segid 77 This will model the strokes as WM hypointensities On 09/07/2017 11:54 AM, miracle ozzoude wrote: > Hello FreeSurfer expert, > > I have a binarized stroke masks of 200 stroke patients that

Re: [Freesurfer] Unknown regions in cortical parcellation

what version of FS are you using? On 09/07/2017 03:19 PM, Aidan Murphy wrote: > > We're running QA on Freesurfer's aseg and aparc+aseg volumes. On the > aparc volume we're noticing fairly large unknown regions in what > should be entorhinal cortex, specifically where it comes up against > the

Re: [Freesurfer] Cluster-Defining Threshold of p=0.025

If you want to use that threshold, you will have to create tables for that threshold using mri_mcsim. See https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo Alternatively, I have a version of mri_glmfit-sim that will run permutation with non-orthogonal designs.

Re: [Freesurfer] combining a stroke lesion label with aseg.presurf.mgz

sorry, should be mergeseg --src aseg.auto.mgz --merge stroke.mgz --o aseg.presurf.mgz --segid 77 when you re-run recon-all, it will create the manedit file On 09/07/2017 12:49 PM, miracle ozzoude wrote: > Thanks doug. If I run the recon-all -autorecon2-noaseg -autorecon3. > Will it

[Freesurfer] 答复: 答复: ROI

Thanks, I will try later. Bo 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 代表 Bruce Fischl 发送时间: 2017年9月7日 4:56:23 收件人: Freesurfer support list 主题: Re: [Freesurfer] 答复: ROI Hi Bo have you