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help > Freesurfer Native Space and Seed to Voxel Analysis
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Jun 22, 2018 12:06 AM | Benson Stevens
Freesurfer Native Space and Seed to Voxel Analysis
Hello Everyone,
I was given freesurfer data processed with the recon-all function. Everything is in native space, aligned with each subjects own orig.gmz as well as T1. I also created a bunch of surface ROI's that were converted to volume space and also aligned. I also aligned all the native space fMRI data with it. I have done a ROI-ROI analysis in CONN. However, this doesn't matter if subjects are in native space and not normalized into some common space. I was looking on this forum and found the following thread of someone wanting to use native freesurfer space with CONN. https://www.nitrc.org/forum/message.php?msg_id=15478
However, what I don't understand, is how can a seed to voxel analysis be done with native space images? Subjects are not in alignment with each other, and therefore voxels don't match across people. Would I have to normalize all subjects to the fsaverage to be able to do so, which defeats the purpose of doing anything in native space. That link above suggests you can put in the native space images. Does recon-all create some type of mapping files for each subject to fsaverage that CONN is able to find and use to map each subjects results to the fsaverage during the seed to voxel analysis?
I kindly thank you in advance,
Benson Stevens
I was given freesurfer data processed with the recon-all function. Everything is in native space, aligned with each subjects own orig.gmz as well as T1. I also created a bunch of surface ROI's that were converted to volume space and also aligned. I also aligned all the native space fMRI data with it. I have done a ROI-ROI analysis in CONN. However, this doesn't matter if subjects are in native space and not normalized into some common space. I was looking on this forum and found the following thread of someone wanting to use native freesurfer space with CONN. https://www.nitrc.org/forum/message.php?msg_id=15478
However, what I don't understand, is how can a seed to voxel analysis be done with native space images? Subjects are not in alignment with each other, and therefore voxels don't match across people. Would I have to normalize all subjects to the fsaverage to be able to do so, which defeats the purpose of doing anything in native space. That link above suggests you can put in the native space images. Does recon-all create some type of mapping files for each subject to fsaverage that CONN is able to find and use to map each subjects results to the fsaverage during the seed to voxel analysis?
I kindly thank you in advance,
Benson Stevens
Jun 25, 2018 10:06 PM | Alfonso Nieto-Castanon - Boston University
RE: Freesurfer Native Space and Seed to Voxel Analysis
Hi Benson,
Yes, recon-all creates a set of lh|rh.sphere.reg files, which map each subject vertex (in subject-space) to a common spherical representation (in fsaverage space). CONN is able to use that information (when you select in the Setup.Structural tab a structural file in the FS output directory -e.g. mri/T1.mgz- and you select in Setup.Options the 'surface' analysis-space option) to run surface-based analyses, where all functional data is ported to this common fsaverage space for the "voxel" part of "seed-to-voxel" analyses (and all you need to do during preprocessing is have your functional data in the same space as your structural FS-processed anatomical data, which sounds like you already have).
Hope this helps
Alfonso
Originally posted by Benson Stevens:
Yes, recon-all creates a set of lh|rh.sphere.reg files, which map each subject vertex (in subject-space) to a common spherical representation (in fsaverage space). CONN is able to use that information (when you select in the Setup.Structural tab a structural file in the FS output directory -e.g. mri/T1.mgz- and you select in Setup.Options the 'surface' analysis-space option) to run surface-based analyses, where all functional data is ported to this common fsaverage space for the "voxel" part of "seed-to-voxel" analyses (and all you need to do during preprocessing is have your functional data in the same space as your structural FS-processed anatomical data, which sounds like you already have).
Hope this helps
Alfonso
Originally posted by Benson Stevens:
Hello Everyone,
I was given freesurfer data processed with the recon-all function. Everything is in native space, aligned with each subjects own orig.gmz as well as T1. I also created a bunch of surface ROI's that were converted to volume space and also aligned. I also aligned all the native space fMRI data with it. I have done a ROI-ROI analysis in CONN. However, this doesn't matter if subjects are in native space and not normalized into some common space. I was looking on this forum and found the following thread of someone wanting to use native freesurfer space with CONN. https://www.nitrc.org/forum/message.php?msg_id=15478
However, what I don't understand, is how can a seed to voxel analysis be done with native space images? Subjects are not in alignment with each other, and therefore voxels don't match across people. Would I have to normalize all subjects to the fsaverage to be able to do so, which defeats the purpose of doing anything in native space. That link above suggests you can put in the native space images. Does recon-all create some type of mapping files for each subject to fsaverage that CONN is able to find and use to map each subjects results to the fsaverage during the seed to voxel analysis?
I kindly thank you in advance,
Benson Stevens
I was given freesurfer data processed with the recon-all function. Everything is in native space, aligned with each subjects own orig.gmz as well as T1. I also created a bunch of surface ROI's that were converted to volume space and also aligned. I also aligned all the native space fMRI data with it. I have done a ROI-ROI analysis in CONN. However, this doesn't matter if subjects are in native space and not normalized into some common space. I was looking on this forum and found the following thread of someone wanting to use native freesurfer space with CONN. https://www.nitrc.org/forum/message.php?msg_id=15478
However, what I don't understand, is how can a seed to voxel analysis be done with native space images? Subjects are not in alignment with each other, and therefore voxels don't match across people. Would I have to normalize all subjects to the fsaverage to be able to do so, which defeats the purpose of doing anything in native space. That link above suggests you can put in the native space images. Does recon-all create some type of mapping files for each subject to fsaverage that CONN is able to find and use to map each subjects results to the fsaverage during the seed to voxel analysis?
I kindly thank you in advance,
Benson Stevens
Jun 27, 2018 05:06 AM | Benson Stevens
RE: Freesurfer Native Space and Seed to Voxel Analysis
Hi Alfonso,
First off, thank you for all your work and keeping up with this great tool. It twas grand to hear back from you and the explanation of the freesurfer part. It was bothering me since I couldn't find it in the manual or the forum - all the way explained. I figured, or assumed, it was pulling those files, but it is great CONN does find them and use them. It would be so much more work at this moment for me if not. Its running now.
Many Blessings,
Benson
First off, thank you for all your work and keeping up with this great tool. It twas grand to hear back from you and the explanation of the freesurfer part. It was bothering me since I couldn't find it in the manual or the forum - all the way explained. I figured, or assumed, it was pulling those files, but it is great CONN does find them and use them. It would be so much more work at this moment for me if not. Its running now.
Many Blessings,
Benson