[Freesurfer] Longitudinal hippocampal subfields analysis

Dear all, I set out to perform a longitudinal analysis of hippocampal subfields. I have already edited the cross and/or the bases when necessary and obtained the longs. Then I have obtained the hippocampal subfields by the automated pipeline: recon-all -s -hippocampal-subfields-T1. Now I am goi

[Freesurfer] LME : longitudinal correlations between imaging and cognition scores

Dear Freesurfer's experts, I have searched through the mailing list but haven't found any answer to my question. Is it possible with LME model to make correlations between for example cortical thickness surface data and cognition scores along time ? As it is possible to test for interaction of gr

[Freesurfer] REPOSTED: 3.5 year Postdoc in Social Neuroscience at Bangor University, UK

***Note: I will be attending the VSS meeting in Florida. If you are attending the meeting and would like to meet to discuss this post, please contact me to arrange a time!*** Applications are invited for a 3.5-year, full time postdoctoral position with Dr. Kami Koldewyn in the Developmental So

Re: [Freesurfer] TRACULA tract reconstruction

Hi Anastasia, Ok thanks a lot! I will download the 6.0 version. Best, Joëlle De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Joëlle Ismay Rosanne Van Der Molen Envoyé : mercredi 3 mai 2017 13:39:34 À : Freesurfer support list Objet : Re: [Freesur

[Freesurfer] Reminder: Fully Funded PhD Studentship in Social Neuroscience at Bangor University, UK {Disarmed}

***Note: I will be attending the VSS meeting in Florida. If you are attending the meeting and would like to meet to discuss this post, please contact me to arrange a time!*** Join the Developmental Social Vision Lab as a PhD Student! Applications are invited for a 3-yea

[Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Hi all, I need a volume that maps my sulci. So first I've run recon-all on my data. Worked like a charm. Visual verification in freeview shows that the inflated surface looks just about right (although it does not seem to be registered to the aparc+aseg volume). However, when I try to run mri_

Re: [Freesurfer] recon-all freezes while CORRECTING DEFECT 60

Dear Bruce, Thank you for your help. I was able to view the defects. It does seem to be an extensive defect—possibly retained dura? I’m not sure of any other way to fix it. Do you think that the poor quality of the source image makes it impossible to generate any kind of surface using free surf

Re: [Freesurfer] Question of longitudinal processing

Hi Martin, Do you mean by creating this long.testretest.qdec file, one can then perform the stats for the longitudinal2StageModel? So for a 2 timepoints analysis, eg. TP1 & TP2. the long.testretest.qdec will be looking like this ? fsid fsid-base tp

[Freesurfer] Calculating effect sizes using an older version of Freesurfer

Using Freesurfer 5.3.0, we assessed correlations. between behavioral measures (e.g., working memory, IQ) and grey matter thickness in a single group of participants. We obtained some results - a significant correlation between measure X and cortical thickness in, say, IFG. We would like to include

Re: [Freesurfer] recon-all freezes while CORRECTING DEFECT 60

Hi Dan it depends what your goal is. I think you could get a decent quality recon with an hour two of work, but I'm not sure I would trust thickness estimates from a scan of that quality cheers Bruce On Fri, 12 May 2017, Weisholtz, Daniel S.,M.D. wrote: Dear Bruce, Thank you for your hel

[Freesurfer] How to visualize the result with mri_glmfit and --table aparc flag

Dear FreeSurfer experts I have come across with this issue as I don't know how visualize the result after mri_glmfit done using --table aparc flag instead of --y. Do I use Matlab to do it? Please give me the instructions briefly as I've just started doing this? Any help is appreciated! Warmest r

[Freesurfer] 2 stage model longitudinal data analysis

Hi, I am interested in looking at groups differences (3 groups) in percent thickness change. I want to use mri_glmfit to analyze but I am unclear on what I should include on my fsgd file. Can you please provide an example? Also The example provided on the fswiki under Option mri_glmfit doesn't

[Freesurfer] FW: 2 stage model longitudinal data analysis

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Maria A Infante [minfa...@ucsd.edu] Sent: Friday, May 12, 2017 3:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] 2 stage model longitudinal data analy

Re: [Freesurfer] How to visualize the result with mri_glmfit and --table aparc flag

Dear FreeSurfer Experts One more question I would like to add is how to interpret the output data after running mri_glmfit like beta.mgh, rstd.mgh on Matlab. Thanks so much for your help Regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)9005