Thanks, EH, you’re absolutely right. It’s a typo, probably product of a copy-paste error :-)  I’ll fix it right away.

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of ganmian <ephong93@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, January 5, 2021 at 03:15
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] [Brainstem Substructures] Resolution of the image "brainstemSsLabels.v10.mgz"

        External Email - Use Caution        

Hi,

I am using a FreeSurfer v6.0 to analyze volumetric features of brainstem substructures.

While reading the document about brainstem module (BrainstemSubstructures - Free Surfer Wiki (harvard.edu)), I was confused by the following sentence:

| brainstemSsLabels.v1x.mgz: the volume with the segmentation at 0.333 mm resolution

because if I load the file "brainstemSsLabels.v10.mgz" using nibabel and check the zoom, it seems to have 0.5 mm resolution.

The following is the result of my code:

>> img = nib.load('brainstemSsLabels.v10.mgz')

>> print(img.affine)

[[ -0.5   0.    0.   43. ]
 [  0.    0.    0.5 -39. ]
 [  0.   -0.5   0.   33. ]
 [  0.    0.    0.    1. ]]

>> print(img.header.get_zooms())

(0.5, 0.5, 0.5)

>> print(img.header)

<class 'nibabel.freesurfer.mghformat.MGHHeader'> object, endian='>'
version      : 1
dims         : [170 201 138   1]
type         : 3
dof          : 1
goodRASFlag  : 1
delta        : [0.5 0.5 0.5]
Mdc          : [[-1.  0.  0.]
 [ 0.  0. -1.]
 [ 0.  1.  0.]]
Pxyz_c       : [  0.5   -4.5  -17.25]
tr           : 0.0
flip_angle   : 0.0
te           : 0.0
ti           : 0.0
fov          : 0.0
 
I wonder if the description of the document is not correct. Could you please check if which is correct?
 

My environment is as follows:

- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

- OS: Ubuntu 18.04
 
Thank you!
 
Best regards
Eunpyeong Hong