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Hello FreeSurfer Developers, I am attempting to use the inverse of the final m3z registration file produced by mri_cvs_register to take files in mni152 space back into my subject's space. I used mri_vol2vol with the --inv-morph flag to accomplish this. However, the resulting outputs produce images with abnormal warpings to the brain. Using mri_vol2vol to take subject files into mni152 space with the same m3z file works fine, it seems to be the inverse that is the problem. Does anyone have thoughts on how I can remedy this issue?
FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1 Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS
Thank you! Noriana Jakopin
External Email - Use Caution
Hello, I just wanted to follow up on this and see if anyone had any suggestions, as I still have not resolved the issue.
Best, Noriana Jakopin
On Tue, Aug 18, 2020 at 12:54 PM Noriana Jakopin nejakopin1@gmail.com wrote:
Hello FreeSurfer Developers, I am attempting to use the inverse of the final m3z registration file produced by mri_cvs_register to take files in mni152 space back into my subject's space. I used mri_vol2vol with the --inv-morph flag to accomplish this. However, the resulting outputs produce images with abnormal warpings to the brain. Using mri_vol2vol to take subject files into mni152 space with the same m3z file works fine, it seems to be the inverse that is the problem. Does anyone have thoughts on how I can remedy this issue?
FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1 Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS
Thank you! Noriana Jakopin
Can you try using mri_convert? Like, mri_convert mni152.nii.gz --apply_inverse_transform xform.m3z subject.mgz Let me know if that works
On 9/8/2020 8:28 PM, Noriana Jakopin wrote:
External Email - Use Caution
Hello, I just wanted to follow up on this and see if anyone had any suggestions, as I still have not resolved the issue.
Best, Noriana Jakopin
On Tue, Aug 18, 2020 at 12:54 PM Noriana Jakopin <nejakopin1@gmail.com mailto:nejakopin1@gmail.com> wrote:
Hello FreeSurfer Developers, I am attempting to use the inverse of the final m3z registration file produced by mri_cvs_register to take files in mni152 space back into my subject's space. I used mri_vol2vol with the --inv-morph flag to accomplish this. However, the resulting outputs produce images with abnormal warpings to the brain. Using mri_vol2vol to take subject files into mni152 space with the same m3z file works fine, it seems to be the inverse that is the problem. Does anyone have thoughts on how I can remedy this issue? FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1 Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS Thank you! Noriana Jakopin
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Noriana Jakopin