[Freesurfer] why same structure has two different volume in aseg.stats and wmparc.stats, for example: amygdala.

Hi freesurfer experts, why same structure has two different volume in aseg.stats and wmparc.stats , for example: amygdala. thanks for your reply! LJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

Re: [Freesurfer] why same structure has two different volume in aseg.stats and wmparc.stats, for example: amygdala.

because the partial volume estimates are different. Use the aseg.stats On Tue, 6 Apr 2010, liyari5018 wrote: > Hi freesurfer experts, > > why same structure has two different volume in aseg.stats and wmparc.stats > , for example: amygdala. > > > thanks for your reply! > > LJ > __

[Freesurfer] Rawavg wrong

Hello, I was wondering whether you could help me wit this. I had reported a talairach error during recon and was asked to check what the rawavg looked like. Sagital is shown instead of Coronal, and upside down at that! Clearly, there is some formatting error. Is there a way to fix this within Frees

Re: [Freesurfer] radiologic convention ?

If you don't have a .mat file, it will assume that it is in radiological order. You can bring it up in tkmedit to verify (it displays in radiological convention). doug rida...@mail.med.upenn.edu wrote: > Hello All, > > If my input images are in Analyze format in Radiologic convention, does >

Re: [Freesurfer] Is this longitudinal result correct

Hi Guang, what do you mean with 'longitudinal brainmask'? You need to overlay the segmentation to the brainmask in the longitudinal subject dir. The brainmask in the base dir is in a different space. Best Martin On Apr 6, 2010, at 11:29, Guang Zeng wrote: Hi, there, I ran the freesurfe

[Freesurfer] How to convert a cortical thickness map to a NIFTY file

Hi, I have a question regarding how to convert a cortical thickness map (i.e. lh.thickness) to a NIFTY file. I have a subject called 'subjid' and I run recon-all on it. So I got the ?h.thickness files. Does freesurfer provide a tool to convert the surface file to a nifty file? I tried using the

Re: [Freesurfer] Is this longitudinal result correct

Hello, Martin Yes, the longitudinal brainmask I meant is the brainmask.mgz in the longitudinal dir, not from the base template. Thanks! Guang From: mreu...@nmr.mgh.harvard.edu To: freesurfer...@hotmail.com Date: Tue, 6 Apr 2010 12:27:19 -0400 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Fr

Re: [Freesurfer] Is this longitudinal result correct

Hm, the brainmask is mapped from the base to the individual TP space and then the T1 image of the TP is masked to create the brainmask for the specific TP. That means the brainmask should look exactly like the T1 for all voxel within the mask. (And therefore very similar to the orig, except for in