All,
I have a question regarding the required registration file in mri_vol2surf.
I have some spherical ROI's in MNI space produced via 3dUndump--they're volume files that show up in the correct places when loaded in with an MNI standard subject such as fsaverage.
I also have some patients scans. I'd really like to compute cortical thickness for these ROI's on my patient scans, so I attempt to follow the instructions at ( https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ), but these instructions assume that the ROI is in the native space--which produces no problems until the step :
cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf \ --mov /path/to/ROI5.nii \ --reg TT_avg152T1_to_fsaverage.dat \ --projdist-max 0 1 0.1 \ --interp nearest \ --hemi lh \ --out lh.fsaverage.ROI5.mgh \ --reshape
My question is then three parts:
(1) Why does vol2surf require a registration file? Shouldn't it be possible to do it as a straight conversion of data types if I know that my surface is registered to the file that I want? Perhaps naive, my first intuition was to construct a TT.dat that was the identity matrix, but this fails, with the response listed in (2).
(2) How can I do this without shifting my data? If I follow the instructions, when the surface is overlayed on fsaverage's lh.pial, the entire surface is included in the overlay.
(3) What exactly do the numbers mean in the registration file TT.dat (as in the instructions on the website)? The 4x4 matrix is clear, and the first two numbers appear to have something to do with Voxel resolution, but I'm unable to find documentation that explains the notation in the output.
Any help anyone can offer would be tremendously appreciated.
-qf
Houston Methodist. Leading Medicine.
Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.
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Hey there
I think you just need to use "--regmethod subject" instead of specifying a registration .dat file. I had similar troubles a few months ago as my labels were made on the volume and I simply wanted to overlay them onto their surfaces in Freesurfer and didn't want any transformation to be made.
Best wishes
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jul 27, 2016 at 12:07 PM, Funk, Quentin qfunk@houstonmethodist.org wrote:
All,
I have a question regarding the required registration file in mri_vol2surf.
I have some spherical ROI's in MNI space produced via 3dUndump--they're volume files that show up in the correct places when loaded in with an MNI standard subject such as fsaverage.
I also have some patients scans. I'd really like to compute cortical thickness for these ROI's on my patient scans, so I attempt to follow the instructions at ( https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ), but these instructions assume that the ROI is in the native space--which produces no problems until the step :
cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf \ --mov /path/to/ROI5.nii \ --reg TT_avg152T1_to_fsaverage.dat \ --projdist-max 0 1 0.1 \ --interp nearest \ --hemi lh \ --out lh.fsaverage.ROI5.mgh \ --reshape
My question is then three parts:
(1) Why does vol2surf require a registration file? Shouldn't it be possible to do it as a straight conversion of data types if I know that my surface is registered to the file that I want? Perhaps naive, my first intuition was to construct a TT.dat that was the identity matrix, but this fails, with the response listed in (2).
(2) How can I do this without shifting my data? If I follow the instructions, when the surface is overlayed on fsaverage's lh.pial, the entire surface is included in the overlay.
(3) What exactly do the numbers mean in the registration file TT.dat (as in the instructions on the website)? The 4x4 matrix is clear, and the first two numbers appear to have something to do with Voxel resolution, but I'm unable to find documentation that explains the notation in the output.
Any help anyone can offer would be tremendously appreciated.
-qf
Houston Methodist. Leading Medicine.
Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
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
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.
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.kuhn@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
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.kuhn@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.
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.kuhn@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.kuhn@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@nmr.mgh.harvard.edu
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Douglas Greve -
Funk, Quentin -
Matyáš Kuhn -
Thomas Yeo -
Trisanna Sprung-Much