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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Ruopeng Wang
Sent: Monday, September 16, 2019 11:51 AM
To: 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@01D56C87.359CC930][cid:image002.jpg@01D56C87.359CC930]
Brainmask.mgz opened only in a new terminal. Rotated and looks smoother than
brainmask above.
[cid:image003.jpg@01D56C87.359CC930]
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
