Re: [Freesurfer] Convert aseg.mgz to .nii and into MNI space with FSL dimensions - Freesurfer

15 Feb 2013


      mri_label2vol will take segmentations as an input look at the --help
doug
On 02/15/2013 04:25 PM, Roderick McColl wrote:
...
Sorry for the bother, but there isn't a label for L or R WM.
Should I use mri_vol2vol on the aseg.mgz file and the mni152.register.dat
file instead i.e. just register aseg.mgz into MNI152 space?
Not sure how to make this use a nearest neighbor interpolation though.
Thanks
-roddy
-----Original Message-----
From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu]
Sent: Friday, February 15, 2013 3:04 PM
To: Roderick McColl
Subject: Re: Convert aseg.mgz to .nii and into MNI space with FSL dimensions
In that case, use mri_label2vol with the following reg $FREESURFER_HOME/average/mni152.register.dat
doug
On 02/14/2013 11:02 AM, Roderick McColl wrote:
...
Thanks very much.
I should have made myself clearer.
I would like to use $FREESURFER_HOME/subjects/fsaverage/mr/aseg.mgz
for some analysis in MNI512 (FSL) space.
So should I use mni152reg on the orig.mgz file in that folder to generate the transform?
-roddy

From: Douglas N Greve [greve@nmr.mgh.harvard.edu]
Sent: Wednesday, February 13, 2013 4:48 PM
To: Roderick McColl
Cc: 'Clark Fisher'; freesurfer@nmr.mgh.harvard.edu
Subject: Re: Convert aseg.mgz to .nii and into MNI space with FSL
dimensions
you can use mni152reg to compute the registration to the MNI152 space.
Make sure to spec the 1mm target. You can then use mri_label2vol to
map aseg.mgz to the MNI152 space.
doug
On 02/13/2013 03:40 PM, Roderick McColl wrote:
...
Hello all,
I have a need to generate LH and RH WM masks for analysis.
I can convert aseg.mgz to aseg.nii but the dims are 256x256x256 and I
need to use the FSL MNI format which is 182x218x182.
Is there a recipe for cropping / translating etc to match the
aseg.mgz atlas with the FSL atlases?
Thanks
-roddy


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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/