The Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz comes from http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011, and the description says it is the FSL MNI152 1mm template interpolated and intensity normalized into a 256 x 256 x 256 1mm-isotropic volume (obtained by putting the FSL MNI152 1mm template through recon-all ). So I supposed it is in MNI305 after it was processed with freesurfer. When I overlap the Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz and Template_T1_IXI555_MNI152.nii it is really shifted so I think it is not in MNI152.
When I add the --invertmtx then the result is still the same, empty image.
I uploaded those images here: https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question.zip , if you want to try yourself.
Thank you,
Matyas
Dne 2.8.2016 v 14:55 Douglas Greve napsal(a):
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 ( ) 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,
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