[Freesurfer] Question about the volume conversion in freesurfer

Dear freesurfer experts, I want to compute functional connectivity based on the region with significantly different cortical thickness of two groups. The fMRI data have been preprocessed by using SPM software and normalized to the MNI space. However, I do not how to use the function mri_surf2vo

Re: [Freesurfer] possible bug in mri_robust_register

Hi Martin, Excellent, it works just fine without the --initorient. However, I'd be happy to help test the fixed version. I'm running the stable v5.3 linux distribution (actual OS is Debian 'jesse' 8.1). Thanks, Andrew On Wed, Sep 23, 2015 at 11:12 PM wrote: > Hi Andrew, > > yes, something is w

[Freesurfer] mri_vol2vol binary mask

Hello, I am try to convert some binary mask (0,1) to native space. I use this command line: mri_vol2vol --mov bin_mask.mgz --targ rawavg.mgz --regheader --o bin_mask _rawavg.nii.gz –no-save-reg I found some result of “ bin_mask _rawavg.nii.gz” with intensity of 0.988 instead of 1. Is there som

[Freesurfer] Fwd: help with trac prep opening bvals within dmri folder

-- Forwarded message -- From: Karuna Subra Date: Wed, Sep 23, 2015 at 7:33 PM Subject: help with trac prep opening bvals within dmri folder To: freesurfer@nmr.mgh.harvard.edu Cc: Brandon Brizendine HI Anastasia, I've been having issues with the trac-prep script. Below is the f

Re: [Freesurfer] sulc

Hi Angela you can load it into matlab with read_curv. If you have the surface and the tal xform (or transform the surface before loading it into matlab) you can find the point on the surface that is closest to a given tal coord and read out the sulc at that point cheers Bruce On Wed, 23 Sep 20

Re: [Freesurfer] [FreeSurfer] Axis of Alignment

You can set the image semi-transparent and use the transformation tools on the Transform Volume window to align it with the reference image. Ruopeng > On Sep 23, 2015, at 5:22 PM, fmri wrote: > > how do you get all the image files to align with the one that you realign ? > > On Aug 11, 2015,

[Freesurfer] Freeview scrolling speed?

Hi all, With Freesurfer 5.3 installed on a OS X 10.10.5 mac (MacBook Air 1.6Ghz i5, 4GB ram), I find that scrolling through slices in Freeview is VERY slow compared to tkmedit when surfaces are loading in addition to 1-2 volumes (e.g., when editing pial/WM segmentations). Any tricks/tips/help to

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

Hi Martin, Thanks for clarifying. As a follow-up, is it ok to use age or mean centered at each scan as the timing variable with the two-stage model? Regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney

Re: [Freesurfer] [FreeSurfer] Axis of Alignment

how do you get all the image files to align with the one that you realign ? On Aug 11, 2015, at 12:07 PM, Ruopeng Wang wrote: > Hi Joseph, > > In freeview you can use "Tools"->"Transform Volume" to reorient volumes. > > Best, > Ruopeng > > On 08/11/2015 02:59 PM, Bruce Fischl wrote: >> Ruopeng

[Freesurfer] sulc

Hi all, is there any way (different from manually looking in tksurfer) to know the value of 'sulc' (or other) in a particular point Talaraich xyz of a subject? Thank you! Angela ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

Re: [Freesurfer] possible bug in mri_robust_register

Hi Andrew, yes, something is wrong with the --initorient you can simply drop it, it registers fine without it. There are non-linearities in your image, so maybe you want to add --affine to get it match better (depending on what this is and what you are using this for). Ha, just found the bug.

Re: [Freesurfer] PET tools in FS dev v6.0

Hi Jonathan just a warning that Doug is likely to be out of contact for a few days so please repost this type of question sometime next week. cheers Bruce On Wed, 23 Sep 2015, Jonathan DuBois wrote: Hi Doug,  Thanks for sending me this information. I ran gtmseg, and bbregister successfully

Re: [Freesurfer] PET tools in FS dev v6.0

Hi Doug, Thanks for sending me this information. I ran gtmseg, and bbregister successfully (I inspected both and they look accurate), but I am getting a s egfault with mri_gtmpvc at the auto mask step. I copied the command and the error below. I thought that it could be a memory issue due to the

[Freesurfer] possible bug in mri_robust_register

Hello all, I've encountered a potential bug in mri_robust_register. For a particular pair of source and target volumes the command: mri_robust_register --satit --initorient --lta robustreg.lta --mov source.mgz --dst target.mgz fails with the following error message: mri_robust_register: Registr

[Freesurfer] qdec error

Dear Experts, I tried to see if the average area/thickness differ between the 2 groups (HC and A) with IQ, Age and Gender as covariates using Qdec, but encountered the error (pls see attached). I tried the same thing for comparison between A and PC and it works fine... please kindly help? Man

[Freesurfer] Call for Papers - Special Issue on Neurofeedback and Functional Enhancement / Neuroscience

CALL FOR PAPERS Society of Applied Neuroscience Neuroscience Special Issue on Neurofeedback and Functional Enhancement: Mechanisms, Methodology, Behavioural and Clinical Applications Aims and Scope Neurofeedback and neuromodulation have become an important tool of modern neurosciences to study f

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

Hi Bronwyn, what Doug indicates here is that he thinks it is possible to do an ANOVA style analysis from a single FSGD and command (something like this: https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova ) But this would not be good in situations where you have different many tim

[Freesurfer] import FS-FAST results in FSL

Hi list, I would like to import FS-FAST results in FSL, opening them by fslview.Could you provide me some suggestion? Thank you very much Stefano___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinf

Re: [Freesurfer] Using external software to perform brain extraction

Hi Richard, yes, that all sounds good to me. The other thing you can do if you have the data is use a T2 or flair to improve the dura removal. cheers Bruce On Wed, 23 Sep 2015, Parker, Richard wrote: Greetings Freesurfer Gurus, I'm having a little trouble with a small minority of my s

[Freesurfer] Using external software to perform brain extraction

Greetings Freesurfer Gurus, I'm having a little trouble with a small minority of my subjects whereby dura is being classed as cortical surface . I've played around with gcut and the watershed parameters, but have so far been unable to achieve a satisfactory cleanup. Before I give up and inve

[Freesurfer] Error from Generating mean value for clusters that survived multiple comparison correction in QDEC

Dear FreeSurfer experts, Am working on this machine: *FREESURFER_HOME: /usr/local/freesurferBuild stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0Debian version: jessie/sidKernel info: Linux 3.19.0-28-generic x86_64* Am trying to extract the mean LGI value for a cluster from QDEC using m

[Freesurfer] R: R: Re: R: Re: R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

For some subject, analysis run fine.For others subjects (processes are the same for all) I have this error fcseed-sess -s Sess001 -cfg MRS_MASK.configmri_label2vol --seg /Applications/freesurfer/subjects/subject_prova/Control01/mri/MRS_MASK.mgz --reg /Applications/freesurfer/subjects/subj/Sess