One possibility is the header information. I looked at the header information and they are not exactly the same between the template and atlas. Perhaps you can try the following:
>> mri_convert --targ Template_T1_IXI555_MNI152.nii --mov >> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz >> --regheader --interp nearest --o Yeo2011_headerfixed.nii.gz Please note that this would involve a nearest interpolation. Hope this would work. --Thomas On Thu, Aug 4, 2016 at 7:06 PM, Matyáš Kuhn <matyas.k...@gmail.com> wrote: > Hi, > > I was using Mango and MriCron to view the results. But you are right that in > freeview it looks just fine :) I saved the yeo atlas image as nifti and it > is now looking well also on mango and MRIcroN. So I suppose that the problem > was with analyze format. > > Thank you all for the help :) > > Matyas > > > Dne 3.8.2016 v 4:43 Thomas Yeo napsal(a): > > Hi Matyas, > > In freeview, looks fine to me. See attached. > > Can you send us your screenshot? > > Regards, > Thomas > > On Tue, Aug 2, 2016 at 9:39 PM, Matyáš Kuhn <matyas.k...@gmail.com> wrote: > > 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, > > Matyas > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
