Many MRI steps only work if the scans are roughly aligned with the MNI template. Rotations (pitch) in particular is difficult to compensate for.
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Approach: all scans get manually aligned
Starting point
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,
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you can choose to manually reorient the scan to align with the template. Specifically,
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you can determine the 6 rigid-body parameters
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for the coregistration (6 parameters = x/y/z shift, and rotations about each axis).
The scan only needs this doing once, even if it’s in multiple projects or multiple groups in a project.
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
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when the Project “Copy and Coreg” is done (before preprocess).
Step 1: copy from raw nifti folder to “rawimeages” project folder
Step 2: if parameters are associated with this scan, apply them (i.e., coreg the scan)
A file “coregister2mni_completed.mat” will be saved (e.g., U:\OSA2019pre\rawimages\OSA\OSA5020\T1w_MPR)E50200220191204S12\Nifti\coregister2mni_completed.mat)
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.
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Example of new GUI (see Step-by-Step Instructions for details)
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Up to Sep 2020
T1
Gets manually aligned in project folder Legacy - Manually Aligning T1's to MNI
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