Re: [Freesurfer] segmentation problem.

Can you try it without the expert opts? And what sequence is the data? On Nov 12, 2012, at 3:35 AM, youngmin huh ymin1...@gmail.com wrote: Hi I'm working with some images, and freesurfer didn't properly detect some of their white matter boundaries. I attached some examples. I ran recon2

[Freesurfer] volume conversion problem

Dear FS experts, I'm trying to convert one skull-stripped image from the FS segmentation to a nifti in native space, but I'm having some troubles with it.I'm doing everything with the a to d stepsa) cd /root/trabajo/freesurfer/subjects/s00x/mri/b) mri_vol2vol --interp nearest --mov brain.mgz

Re: [Freesurfer] pre-processing functional data error

/Run this command line instead mri_convert.linux I0001.dcm s105.run1.nii/ doug On 11/09/2012 01:57 PM, Yangmei LUO wrote: Hi Dr, Douglas, I attached the capture of the result using fslview. Thanks very much! Yangmei On Fri, Nov 9, 2012 at 12:51 PM, Yangmei LUO yangmei...@gmail.com

Re: [Freesurfer] volume conversion problem

Can you send the result of mri_info brain.mgz mri_info rawavg.mgz doug On 11/12/2012 10:27 AM, Gabriel Gonzalez Escamilla wrote: Dear FS experts, I'm trying to convert one skull-stripped image from the FS segmentation to a nifti in native space, but I'm having some troubles with it. I'm

Re: [Freesurfer] pre-processing functional data error

sorry, remove the slash from the end of the line On 11/12/2012 10:49 AM, Yangmei LUO wrote: Hi Douglas, Thank you for your kind help. The command still can not work. $ /usr/local/freesurfer/bin/mri_convert.linux I0001.dcm s105.run1.nii/ /usr/local/freesurfer/bin/mri_convert.linux I0001.dcm

[Freesurfer] The mismatched color in the tksurfer color bar for surface file

Hi, Doug and other FreeSurfer experts: I noticed that the color in a surface file I generated (*.mgh with the values ranging from 0 to 1) does not match that in the color bar. For example, the lowest value in the surface file has much darker red hue than the lowest values in the color bar

Re: [Freesurfer] volume conversion problem

Here yu are:mri_info brain.mgzVolume information for brain.mgz  type: MGH    dimensions: 256 x 256 x 256   voxel sizes: 1., 1., 1.  type: UCHAR (0)   fov: 256.000   dof: 0    xstart: -128.0, xend: 128.0    ystart: -128.0, yend: 128.0   

Re: [Freesurfer] segmentation problem.

Thanks. I'll try without expert opts. But i'm not sure if i can get better results. Before I found out these expert opts, I ran some images recon2 without expert opts. And they got poor segmentation. Actually, some images showed improvement with those options. I'm curious why these options work

Re: [Freesurfer] bad acquisition and noise problem.

Hi, 3D SPGR sequences were used. (TR=22, TE=4, thickness=1.4, FOV=240*240, FA=40) If the artifacts are due to B0 distortion, I wonder how I can fix it. Thanks, Youngmin Huh 2012/11/12 Bruce Fischl fis...@nmr.mgh.harvard.edu Can you give us the acquisition details? I suspect this is not

Re: [Freesurfer] bad acquisition and noise problem.

Are you using a 32-channel coil? It looks like B1- receive field inhomogeneity to me. Peace, Matt. From: youngmin huh ymin1...@gmail.com Date: Monday, November 12, 2012 10:22 PM To: Bruce Fischl fis...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bad