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Sep 2020 Onwards
T1 Legacy
Gets manually aligned in project folder Manually Aligning T1's to MNI
All scans
Determine manual coregistration parameters, and automatically apply.
All MRI studies can have a coregistration from the original nifti (as converted in CSPM) to overlap MNI space. The parameters are determined for each scan, although these can be copied across scans and studies.
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Approach: all scans get manually aligned
Scans are manually converted to nifti in the raw data folder.
Each scan is linked to a “study”, and this study is added to one or more projects.
At the project level, a person can choose manually reorient the scan. Specifically, they determine the 6 rigid-body parameters that will move the raw scan into a alignment with the template.
Those parameters are saved in the database, and they are associated with the study.
Rationale: One scan = one alignment. If the study is used in multiple projects, the same parameters will be reused. Additionally, if a second preprocessing is done, that will also use the same parameters.
CSPM will apply the parameters after the files are copied from the raw folder to the project preprocessing folder.
Each scan is aligned separately. However, it’s easy to copy the same parameters between scans (useful if one subject has 10 scans with the same rotation, for example).
Rationale: problems arise if we assume that one subject has the same rigid-body shifts for all scans. This approach is more time-consuming, but simple and reliable.
How-to
Example of new GUI
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Up to Sep 2020
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Gets manually aligned in project folder Legacy - Manually Aligning T1's to MNI
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