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) https://secure-web.cisco.com/1S-b5rCCfiUM_20r5cYkwhXu2P25IPqutTefsWepu1yx8D1uhgvv7N8jQuEdjzftjq9ydEVyvVXxU2fZ2l1kFlHEqET8YaKkdQotZta9PAJyy40DJLsHC6BaEh9pmWmKsCHcEjUcMNPoTzbwz2esye-GlrRZLjLU7-VEj8QaaSrnrlInDxRr-UcCzvs7KiswzvCkOj4vP2rxobcNe7fxlFW3SA6PNy75biKunGqQBGxskkl-kSTJAy1e_55FWoriiG4tqaxZIZwX6E5XL97U3NA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBrainstemSubstructures), 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
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)https://secure-web.cisco.com/1S-b5rCCfiUM_20r5cYkwhXu2P25IPqutTefsWepu1yx8D1uhgvv7N8jQuEdjzftjq9ydEVyvVXxU2fZ2l1kFlHEqET8YaKkdQotZta9PAJyy40DJLsHC6BaEh9pmWmKsCHcEjUcMNPoTzbwz2esye-GlrRZLjLU7-VEj8QaaSrnrlInDxRr-UcCzvs7KiswzvCkOj4vP2rxobcNe7fxlFW3SA6PNy75biKunGqQBGxskkl-kSTJAy1e_55FWoriiG4tqaxZIZwX6E5XL97U3NA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBrainstemSubstructures), 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
freesurfer@nmr.mgh.harvard.edu
-
ganmian -
Iglesias Gonzalez, Juan E.