Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

On Do, 2018-03-08 at 03:56 +0100, Kaushal, Mayank wrote: > Your inputs have been very helpful. > > Looking at the examples on LME webpage, the contrast for both > univariate and mass-variate creates 3 rows with 14 columns for > univariate and 17 for mass-variate analysis. My understanding is that >

[Freesurfer] Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix

Dear all, I am trying to correlate psychometric measurements and the local Gyrification Index. To do so, I use the FreeSurfer pipeline to calculate the lGI and then PALM, following the advice in this thread (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050703.html). All

[Freesurfer] Brain microstructure MRI postdoc (Italy)

Hello, We will soon advertise a 2-year postdoctoral fellowship at the MRI Group of the Center for Mind/Brain Sciences (CIMeC ), University of Trento , Italy. The focus of this position will involve the deve

[Freesurfer] Mean Curvature

Hej FreeSurfer, Question regarding the meancurv extracted from the Desikan atlas using aparcstats2table. Is the meancurv the absolute mean curvature? Thus all the values are positive? Best regards Kasper Sent from [ProtonMail](https://protonmail.com), Swiss-based encrypted email. Sent with [P

Re: [Freesurfer] Mean Curvature

Hi Kaspar I don't think so. cheers Bruce On Thu, 8 Mar 2018, Kasper Jessen wrote: > Hej FreeSurfer, > > Question regarding the meancurv extracted from the Desikan atlas using > aparcstats2table. > > Is the meancurv the absolute mean curvature? Thus all the values are positive? > > Best regar

[Freesurfer] FreeSurfer Edit Sequence Inquiry

Hello FreeSurfer Group, I am writing to inquire about Editing Sequence. The "Troubleshooting your output" page (https://surfer.nmr.mgh. harvard.edu/fswiki/FsTutorial/TroubleshootingData) explains the edits sequence as brain mask --> wm volume --> white surface --> control points. Do you suggest

Re: [Freesurfer] [Freesurfer/Freeview cutting]

Hi, There is no surface cutting function in freeview. But I’m going to add it. Will let you know when I have it ready for testing. Best, Ruopeng > On Mar 7, 2018, at 11:16 PM, Dave Yas wrote: > > Hello, > > Can we cut the surface (for flatting later) in freeview? if yes, how? I cant > find

Re: [Freesurfer] Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix

can you send your fsgd file so that I have a better idea of what you are mentioning? On 03/08/2018 08:39 AM, k.ohmst...@stud.uni-heidelberg.de wrote: > Dear all, > > I am trying to correlate psychometric measurements and the local > Gyrification Index. > To do so, I use the FreeSurfer pipeline t

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

I created the contrast: CM.C = [1 1 0 0 0 0; 1 1 0 0 0 0] Then I ran the following: F_lhstats = lme_mass_F(lhstats,CM); I received the following error message, which kept on repeating in loop. Warning: Matrix is singular to working precision. > In matlab.internal.math.mpower.viaMtimes (line 35)

Re: [Freesurfer] FreeSurfer Edit Sequence Inquiry

Hi David, There is no particular order in which you have to make edits. The order in which these edits are described on our wiki is not indicative of any order in which they must be made. However, it may help you to understand the overall order of the recon-all processing stream so that you kn

[Freesurfer] Question regarding recon-all

Hello, I am running recon-all for the first time, and I am wondering when it is proper to use the -i option. My current recon-all command includes the -i option: recon-all -i T1.nii.gz -s 1020 -all, where T1.nii.gz is a nifti file of all 160 anatomical dicoms. I've seen some commands like this

Re: [Freesurfer] Question regarding recon-all

Hi Dan yes, we typically use -i and read in the dicoms directly, but you can do it for a nifti also. Or you could create the 001.mgz and not use it, but there is no reason to (it's just more work). cheers Bruce On Thu, 8 Mar 2018, Levitas, Daniel wrote: Hello, I am running recon-all for

Re: [Freesurfer] Question regarding recon-all

Hi Bruce, Thanks for your response. Just to clarify, I can run recon-all with the -i option and not create the 001.mgz file from mri_convert because recon-all will perform the conversion anyway? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of

Re: [Freesurfer] Question regarding recon-all

yes, exactly. On Thu, 8 Mar 2018, Levitas, Daniel wrote: Hi Bruce, Thanks for your response. Just to clarify, I can run recon-all with the -i option and not create the 001.mgz file from mri_convert because recon-all will perform the conversion anyway?

[Freesurfer] Brainstem registration

Dear whomever it may concern, I'm Chungmin, a graduate research assistant in University of Texas at Austin, I'm fairly new to using freesurfer, I'd appreciate to get some advice on what I'm facing, I have fMRI limited FOV collected on brainstem + little cerebellum/visual area, I've tried SPM man

Re: [Freesurfer] Brainstem registration

Hi Chungmin do you have a whole-brain T1 that you can use for generating anatomical models? If so, many more things are possible cheers Bruce On Thu, 8 Mar 2018, Chungmin Han wrote: Dear whomever it may concern, I'm Chungmin, a graduate research assistant in University of Texas at Austin,

Re: [Freesurfer] Mean Curvature

Hej Bruce, Based on the formular for mean curvature stated below and the article by R. Pienaar (https://surfer.nmr.mgh.harvard.edu/pub/articles/AMethodologyForAnalyzingCurvature.pdf) H = 0.5(k1 + k2) i understand the following: k1 is by definition larger than k2. Thus values of H is primarily

[Freesurfer] Negative areas in mris_sphere, dark in freeview

Freesurfer devs, I have a baffling problem in mris_sphere. I have generated some surfaces using an external tool that uses VTK. After converting the surfaces into freesurfer format using a basic format converter, then adding volume geometry to the surface file using the image used to create it