From the names, it looks like both the seg vol and the template vol are both in mni152. Where did Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz come from? One thing you can try is to invert the registration by adding --invertmtx to the command line.
On 8/2/16 8:18 AM, Matyáš Kuhn wrote:
Hi Freesurfer experts,
I just started to use Freesurfer and I was wondering how can I convert images from MNI305 which uses Freesurfer to MNI152 which is used by SPM. We would like to get MNI152 template of Yeo parcelation (http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011) so we can overlay with our results from SPM fMRI analysis.
I tried this: mri_label2vol --seg /path_to_analysis/Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz \ --temp /path_to_analysis/Template_T1_IXI555_MNI152.nii \ --reg $FREESURFER_HOME/average/mni152.register.dat \ --o /path_to_analysis/output_mni152.nii
which resulted in image full of zeros (so maybe problem with registration?). The "Template_T1_IXI555_MNI152.nii" is the MNI152 template which is used by Computational anatomical toolbox 12 for SPM from Christian Gaser and his group.
Thanks in advance for any suggestions,
Matyas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer