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I am using the OpenNeuro dataset "Reconstructing Faces from fMRI Patterns using Deep Generative Neural Networks": https://openneuro.org/datasets/ds001761/versions/2.0.0. In this dataset, four subjects go through eight sessions each, and each session includes an anatomical scan. For each subject, we would like to register all of the functional data across the eight sessions onto a single anatomical image for analysis. Which is a long way of saying yes, this is the same subject scanned at different time points. What is the correct method to register all of the functional images to the same anatomical image?

On Fri, Jun 12, 2020 at 10:29 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Can we back up a moment? Is this the same subject scanned at different time points? If so, why are you using CVS? That is probably not necessary unless there is a lot of anatomical change between the two time points.


On 6/9/2020 3:22 PM, Paul Soulos wrote:

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Hello,


I am trying to solve an issue with reregistering functional images onto a new anatomical. Let’s say I have two anatomical images from sub01-ses01/orig.mgz and sub01-ses02/orig.mgz, as well as functional files each registered to their corresponding anatomical sub01-ses01/fmcpr.nii.gz and sub01-ses02/fmcpr.nii.gz. My goal is to reregister Dsub01-ses01/fmcpr.nii.gz onto the sub01-ses02 anatomical. Screenshots of my issue are available at: https://imgur.com/a/9GDm9yp


To create a mapping between the two anatomical images, I first run:

$ mri_cvs_register --mov sub01-ses01 --template sub-01-ses-02


When I view the output of the mri_cvs_register command, everything is lined up and looks good:

https://i.imgur.com/SvjPVHX.png


Next, I reregister sub01-ses01/fmcpr.nii.gz using the mapping created with mri_cvs_register:

$ mri_vol2vol --noDefM3zPath --mov sub01-ses01/fmcpr.nii.gz --m3z $SUBECTS/sub01-ses01/cvs/final_CVSmorph_to-sub01-ses02.m3z --o sub01-ses01/fmcpr.ses02space.nii.gz --nearest --targ sub01-ses02/orig.mgz


When I view sub01-ses01/fmcpr.ses02space.nii.gz over sub01-ses02/orig.mgz, the functional image is off by 90 degrees. This is unexpected:

https://i.imgur.com/CpGtKyM.png


If I manually rotate the functional image in Freeview by 90 degrees, it looks good:

https://i.imgur.com/SkDNzuK.png


mri_vol2vol has a --rot argument, so I tried to use this to perform the rotation automatically. Rather than 90 degrees, I now have to specify -90 degrees. Unfortunately, the output when I specify the rotation in mri_vol2vol does not line up well with the anatomical.

https://i.imgur.com/vjxV6rv.png



Does anyone know why this is happening? Please let me know if you have any suggestions.


Thank you!

Paul



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