Re: [Freesurfer] Parcelation a2009 as mask for SPM analysis
Hi Doug, Yes I did and the registration looks good to me (no axial shift in the images) - but I am little confused. In the command for check the registration: /tkregister2 --mov $SUBJECTS_DIR/568/mri/mni152.orig.mgz \ --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz \ --reg $SUBJECTS_DIR/568/mri/mni152.orig.mgz.reg / I am comparing images of subject in MNI space and the MNI template, right? Why there is also the registration file? In mri_label2vol I am using /mri/transforms/reg.mni152.2mm.dat for tranform aparc+aseg to MNI. Which transformation to use? Or should I combine somehow the transformations? The result with the ..transforms/reg.mni152.2mm.dat is still shifted. Or should I try some other way to get aparc+aseg to MNI? Thank you for any help, Matyas /PhD student,// //CEITEC MU, Brno// //Czech republic/ Dne 9.9.2016 v 18:53 Douglas Greve napsal(a): Did you verify that the result of mni152reg is accurate? It should have printed out a command line to check it On 9/9/16 5:58 AM, Matyáš Kuhn wrote: Hi FreeSurfer experts, We would like to use Destrieux atlas for masking DLPFC in subjects, who uderwent fMRI and we used SPM to process the data. We want to find peaks in individuals according to some regions from the atlas (create individual mask). The problem I am facing is to get aparc.a2009s+aseg.mgz to MNI space so I could overlay results from SPM and Freesurfer. I followed some discussions on mailing list and tried this: mni152reg --s $SUB mri_label2vol --seg $SUBJECTS_DIR/$SUB/mri/aparc.a2009s+aseg.mgz \ --temp /.../spm/spmT_0001.nii \ --reg $SUBJECTS_DIR/$SUB/mri/transforms/reg.mni152.2mm.dat \ --o aseg.$SUB.mni152.nii The process ended without errors, but while watching results in freeview - the results are not correctly aligned. Is FSL (which is part of mni152reg procedure) using some other MNI template than SPM? Any suggestions will be most appreciated. The freeview snapshot is here: https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question/freeview_a2009s_mni.PNG ___ 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] Parcelation a2009 as mask for SPM analysis
Hi FreeSurfer experts, We would like to use Destrieux atlas for masking DLPFC in subjects, who uderwent fMRI and we used SPM to process the data. We want to find peaks in individuals according to some regions from the atlas (create individual mask). The problem I am facing is to get aparc.a2009s+aseg.mgz to MNI space so I could overlay results from SPM and Freesurfer. I followed some discussions on mailing list and tried this: mni152reg --s $SUB mri_label2vol --seg $SUBJECTS_DIR/$SUB/mri/aparc.a2009s+aseg.mgz \ --temp /.../spm/spmT_0001.nii \ --reg $SUBJECTS_DIR/$SUB/mri/transforms/reg.mni152.2mm.dat \ --o aseg.$SUB.mni152.nii The process ended without errors, but while watching results in freeview - the results are not correctly aligned. Is FSL (which is part of mni152reg procedure) using some other MNI template than SPM? Any suggestions will be most appreciated. The freeview snapshot is here: https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question/freeview_a2009s_mni.PNG ___ 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.
Re: [Freesurfer] Labels to MNI152, SPM compatible
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 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.
Re: [Freesurfer] Labels to MNI152, SPM compatible
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] Labels to MNI152, SPM compatible
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 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.
