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coregister.txt
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coregister.txt
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Coregister
--------------------
* **Subject info**:
* **reference**: Filetype of reference image stored in each subject's folder to register.
* **source**: Filetype of image to match the reference image stored in each subject's folder.
* **seg & bet**: Segment and skull stripe structural T1/T2 image. Using skull striped T1/T2 image for coregistration is recommended.
* **options**:
1: segment using new segment and bet based on tissue probability maps;
2: bet only (there should be segmented :file:`c1-c3\*.nii` files in the directory);
other number: do not segment nor bet; we recommend using :file:`co\*.nii` instead of :file:`bet\*.nii` to normalise.
.. image:: _images/coregister.png
:align: right
* **Estimate**:
* **object fun**: Methods to maximise or minimise objective function.
* **sep**: The average distance between sampled points (in mm).
* **tol**: The accuacy for each paramters.
* **fwhm**: Kernel of gaussian smooth to apply to the 256*256 joint histogram.
* **Reference**: `spm manual`_.
.. _`spm manual`: http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf
- `Preprocess Modules`_
- `Slice Timing`_
- `Realign`_
- `Coregister (optional)`_
- `Normalize`_
- `SPM8`_
- `SPM12`_
- `Denoise`_
- `Smooth`_
.. _`Preprocess Modules`: Preprocess_Modules.html
.. _`Slice Timing`: slice_timing.html
.. _`Realign`: realign.html
.. _`Coregister (optional)`: coregister.html
.. _`Normalize`: normalise_spm12.html
.. _`SPM12`: normalise_spm12.html
.. _`SPM8`: normalise.html
.. _`Denoise`: denoise.html
.. _`Smooth`: smooth.html