[Freesurfer] Getting voxel values from aseg.mgz

After the recon-all process I want to access all the voxels in the left hippocampus ( any subcortical region ) . Please tell me is there any method to extract this voxel values from an segmented image. Thanking you Pradeep Kumar Mahato ___ Freesurfer ma

Re: [Freesurfer] thickness from pial and white

Thanks. I will try mris_fill. Xiaomin From: Bruce Fischl Sent: ‎Tuesday‎, ‎December‎ ‎9‎, ‎2014 ‎4‎:‎31‎ ‎PM To: Freesurfer support list it creates a file in curvature format, yes. Did you try mris_fill for the wm.mgz? It won't be exactly the same as the one we would generate. Yo

Re: [Freesurfer] Modeling cortical thickness question

Do you mean a polynomial of age? If so, just add age age^2 and age^3 as variables in the FSGD file doug On 12/09/2014 02:04 PM, Alexandra Tanner wrote: > Hello Freesurfers, > > Our group is wondering if any of you know whether it is possible to model > cortical thickness as a third order polynom

Re: [Freesurfer] thickness from pial and white

it creates a file in curvature format, yes. Did you try mris_fill for the wm.mgz? It won't be exactly the same as the one we would generate. You could use mris_fill to generate the interior of the ?h.white surface, then use the aseg to remove non-wm voxels I guess On Tue, 9 Dec 2014, Xiaomin Yu

Re: [Freesurfer] thickness from pial and white

Thanks very much. Does this create curvature file? Again, is it possible to generate wm.mgz from those files? Thanks, Xiaomin > On Dec 9, 2014, at 4:19 PM, Bruce Fischl wrote: > > I think just the ?h.white and ?h.pial > > cheers > Bruce >> On Tue, 9 Dec 2014, Xiaomin Yue wrote: >> >> Wha

Re: [Freesurfer] thickness from pial and white

I think just the ?h.white and ?h.pial cheers Bruce On Tue, 9 Dec 2014, Xiaomin Yue wrote: What I mean by inputs is the default files the mris_thickness will be looking for to run correctly  Xiaomin  On Dec 9, 2014, at 1:08 PM, Xiaomin Yue wrote: Hi Bruce, Thanks for your respo

Re: [Freesurfer] Problem with mris_register: face not in vertex face list

seems like the rh.sphere file is corrupted. Maybe you ran out of disk space? I would try deleting it and reruning with -make all cheers Bruce On Tue, 9 Dec 2014, Wegbreit, Ezra wrote: Dear Freesurfer support community, I am having a recurring issue with re-running a participant after making

Re: [Freesurfer] thickness from pial and white

mris_thickness usage: mris_thickness [options] This program measures the thickness of the cortical surface and writes the resulting scalar field into a 'curvature' file file>. valid options are: -max use to threshold thickness (default=5mm) -fill_holes fill in thickness in hole

Re: [Freesurfer] thickness from pial and white

What I mean by inputs is the default files the mris_thickness will be looking for to run correctly Xiaomin > On Dec 9, 2014, at 1:08 PM, Xiaomin Yue wrote: > > Hi Bruce, > > Thanks for your response. What's the inputs to the mris_thickness? I need > the wm.mgz to generate the ratio of g

[Freesurfer] Problem with mris_register: face not in vertex face list

Dear Freesurfer support community, I am having a recurring issue with re-running a participant after making manual white matter edits (i.e., filling in holes in the wm.mgz file). I saved the new wm.mgz file and then reran using -make all (twice). For some reason, Freesurfer stops at the Surf Re

[Freesurfer] Modeling cortical thickness question

Hello Freesurfers, Our group is wondering if any of you know whether it is possible to model cortical thickness as a third order polynomial? The specific question is: we are looking at whether there is a hyperbolic relationship between cortical thickness and date of birth among a cohort of individ

Re: [Freesurfer] thickness from pial and white

Hi Bruce, Thanks for your response. What's the inputs to the mris_thickness? I need the wm.mgz to generate the ratio of gray vs. white matter. Xiaomin Date: Tue, 9 Dec 2014 09:55:21 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness

Re: [Freesurfer] thickness from pial and white

the thickness you can generate using mris_thikness. Why do you want to generate a wm.mgz? I guess you could from the wmparc On Mon, 8 Dec 2014, Xiaomin Yue wrote: Hi All,   Cortical surface reconstructed using caret from a high resolution MRI data (0.25 mm) has been converted to freesurfe

Re: [Freesurfer] Probabilities in the Brodmann area labels

is this in your individual subject space or in fsaverage? On Tue, 9 Dec 2014, pfannmo...@uni-greifswald.de wrote: > Dear FreeSurfer Experts, > > I am puzzeled about the probabilities in the Brodmann area labels. If I take > the Brodmann areas 1, 2, 3a and 3b and add their probabilities at a cert

[Freesurfer] Probabilities in the Brodmann area labels

Dear FreeSurfer Experts, I am puzzeled about the probabilities in the Brodmann area labels. If I take the Brodmann areas 1, 2, 3a and 3b and add their probabilities at a certain vertex a probability sum < 1 should arise. This is due to the fact that 10 brains where analyzed in order to compute

Re: [Freesurfer] Extracting hippocampus

Hi Pradeep sorry, I meant autorecon1 and autorecon2 (but not autorecon3) cheers Bruce On Tue, 9 Dec 2014, pradeep mahato wrote: > Hi Bruce, > > I am using Intel Core 2 Quad core processor 2.2 GHz with 4 GB ram. > The version i am using is freesurfer-i686-redhat-linux-gnu-stable5-20130513 > Usi

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

Dear Doug, I tried to run MCC with cluster-sess but unfortunately I got the same error message like when I'm using mri_glmfit-sim. It does not recognize the thresh (cluster-forming thresh) Here is the terminal output: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /h