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I'm still a little confused. When I open up the brainmask.mgz in freeview I see the following. It is rotated compared to the native 001.mgz below.
[cid:image002.jpg@01D56C9C.9A38CF50]
I then open the 001.mgz with freeview in a NEW terminal (seperate session), I get the following. Should thy not be the same orientation?
[cid:image007.jpg@01D56C9C.9A38CF50]
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ruopeng Wang Sent: Monday, September 16, 2019 1:17 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 001 vs brainmask views in freeview
The first volume is always displayed in its original orientation where pixel data are stored. So that the pixel data don't get resampled (unless you force it with '-r' flag to resample it in standard RAS).
Ruopeng On 9/16/19 1:06 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution Thanks for info.
If I open only the brainmsk.mgz only from a new terminal it is rotated and not in its native orientation (which is 001's orientation). Why does it not appear to be in native space in freeview?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ruopeng Wang Sent: Monday, September 16, 2019 11:51 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 001 vs brainmask views in freeview
Hi,
When you load brainmask.mgz as the second volume, it will be realigned to 001.mgz. The default resample method is nearest-neighbor. Thus you get the blocky look. You can try loading it with trilinear or cubic resampling like this from the command-line:
freeview -v 001.mgz brainmask.mgz -trilinear
Ruopeng On 9/16/19 12:41 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution Hi all,
I ran a 2yo subject through FS6.0 using 'recon-all -i /firstdicom.dcm -all' and the output segmentations and surfaces looks good.
Can someone explain why I see different alignments when I view the 001.mgz and brainmask.mgz files in freeview, depending on the order files are opened.
001.mgz AND brainmask.mgz -- 001 opened first in freeview followed by brainmask.mgz. Alignemnts OK but brainmask looks grainy. [cid:image001.jpg@01D56C9B.65CA38E0][cid:image003.jpg@01D56C9B.65CA38E0]
Brainmask.mgz opened only in a new terminal. Rotated and looks smoother than brainmask above. [cid:image004.jpg@01D56C9B.65CA38E0]
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