[Freesurfer] Visualize cortical projections of fiber pathways using FreeSurfer

Hi, FreeSurfer experts I have a question regarding visualizing the cortical projections of a fiber bundle using FreeSurfer based on the data from a group of subjects. Since I am interested in seeing both the cortical projections on the surface and the trajectory of the fiber bundle derived

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

Hi, Bruce The command line I used is:  mris_fill -r 1 -c rh.white rh.white.nii.gz I attached the rh.white in my previous mail. Could you see it in the attachment? Thank you! Longchuan From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

-c -r 1 lh.white lh.white.nii.gz Thanks Longchuan From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, March 17, 2013 11:47 AM Subject: Re: [Freesurfer] make a volume

[Freesurfer] make a volume template from the surface-based template for non-human primates

Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys and now, we want to see the result, which is a mgh surface file, on the coronal slices of the template. So I

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 15, 2013 4:56 PM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates Hi Longchuan what kind

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, November 21, 2012 3:20 PM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz Hi Longchuan, I'm

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

To: Longchuan Li leonad...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu; Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Tuesday, November 20, 2012 3:19 PM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz Hi Longchuan, mris_fill create

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 19, 2012 8:57 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz Hi Longchuan have you

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

used as the template for motion correction. doug On 11/19/2012 10:30 AM, Bruce Fischl wrote: Hi Longchuan yes, I think you can do this with tkregister2. Doug can give you the details Bruce On Mon, 19 Nov 2012, Longchuan Li wrote: Hi, Bruce Thank you for the information. I will re-run recon

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

On 11/19/2012 10:30 AM, Bruce Fischl wrote: Hi Longchuan yes, I think you can do this with tkregister2. Doug can give you the details Bruce On Mon, 19 Nov 2012, Longchuan Li wrote: Hi, Bruce Thank you for the information. I will re-run recon-all using -cm option to see if the problem

[Freesurfer] the positions of white/pial surfaces and the brain.mgz

Hi, FreeSurfer experts I have a question regarding coregistering white and pial surfaces with the brain.mgz and would appreciate your help on this. I am working on non-human primates and noticed that my white and pial surfaces do not have identical positions as brain.mgz. For example, when I

[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

[Freesurfer] transfer label from high-resolution mesh to low resolution mesh

Hi, all I am trying to transfer some labels on a high-resolution white surface mesh (~100K) to a corresponding low-resolution white mesh(~10K) that is generated using FS function mris_decimate. Could someone tell me what is the most efficient way to realize that? Many thanks in advance!

[Freesurfer] A question about downsmapling mulitple surfaces (white, pial, sphere) for registration

Hi, FreeSurfer experts Currently, I am planning to run tractography using wm surfaces as seed masks and pial surfaces as stop masks implemented in FSL. In order to make fibers go through one hemisphere to another, I need to remove the medial wall from both seed surfaces and the pial surfaces.