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:

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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:

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    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.

    Brainmask.mgz opened only in a new terminal. Rotated and looks
    smoother than brainmask above.

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