Dear FreeSurfer community,
I am trying to obtain subcortical segmentation masks for a group of healthy volunteers using FreeSurfer v5.1 running on Ubuntu 12.10. I need the masks to be in the native space of the original 1mm^3-isotropic 256*256*160 T1-weighted images. I found a helpful link which seems to answer my need:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Running it seems to produce good results when overlaid on top of the original images. However, I couldn't find any mention in either the newsgroups or the wiki as to whether this affects the subcortical masks in any (significant?) way. What sort of differences should I expect between the masks in the "freesurfer space" and the ones converted back to native space? Are there any structures or artifacts I should mindful of?
Thank you!
Assaf
PS Just to make things concrete, assuming I have a patient called Sam, then, after running recon-all, I typed in:
cd $SUBJECTS_DIR/Sam/mri
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz
e.g., for cerebral WM: mri_extract_label aseg-in-rawavg.mgz 2 41 cerebralWMNative.mgh
mri_convert cerebralWMNative.mgh cerebralWMNative.img (this last step is used to create ANALYZE format images which is the format my code is already structured to read out)
maybe sure you specify nearest neighbor interpolation when converting the aseg. You will lose some accuracy with the resampling of course.
cheers Bruce On Fri, 8 Mar 2013, Tal, Assaf wrote:
Dear FreeSurfer community,
I am trying to obtain subcortical segmentation masks for a group of healthy volunteers using FreeSurfer v5.1 running on Ubuntu 12.10. I need the masks to be in the native space of the original 1mm^3-isotropic 256*256*160 T1-weighted images. I found a helpful link which seems to answer my need: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Running it seems to produce good results when overlaid on top of the original images. However, I couldn't find any mention in either the newsgroups or the wiki as to whether this affects the subcortical masks in any (significant?) way. What sort of differences should I expect between the masks in the "freesurfer space" and the ones converted back to native space? Are there any structures or artifacts I should mindful of?
Thank you!
Assaf
PS Just to make things concrete, assuming I have a patient called Sam, then, after running recon-all, I typed in:
cd $SUBJECTS_DIR/Sam/mri
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz
e.g., for cerebral WM: mri_extract_label aseg-in-rawavg.mgz 2 41 cerebralWMNative.mgh
mri_convert cerebralWMNative.mgh cerebralWMNative.img (this last step is used to create ANALYZE format images which is the format my code is already structured to read out)
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Tal, Assaf