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The T1 files to register are in T1_manual2MNI folders. Subject folders in T1preprocess contain three subfolders with T1 files, in the following order (numbers refer to image labels):
- Subject T1preprocess subfolder
- Copies of individual series T1 images (some protocols use multiple T1 scans that are averaged to create a clean image).
- T1_initnative_[N]seriesseriesSingle
- Single T1 in original native space; if more than one series was collected, this file is the average of all series.
- T1_manual2MNI
- A single T1 that can (optionally) be manually registered to the template. This initially is simply a copy of the native T1 (previous step).
- T1_ref_vox...bb...
- A resliced version of the T1; this becomes the reference for native space.
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