.. _spm_lesion_norm_tpm:

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SPM Lesion Normalization with Tissue Probability Maps
=====================================================

| Maintainer: Dianne Patterson Ph.D. dkp @ arizona.edu
| Date Created: 2018_06_25
| Date Updated: 2019_06_26
| Tags: SPM, normalization, standard space, lesion, anat, TPM
| Software: At least Matlab 2016B, SPM12

**Goal**: Warp a native space lesion mask (and optionally a native space anatomical image) into standard (MNI) space. In this procedure we use the lesion mask to define an additional tissue probability map (TPM) that influences the warp.

Data
****

* Images must **not** be zipped (i.e., *T1w.nii* is okay, but *T1w.nii.gz* is not).
* An anatomical (anatomical) image, usually T1 weighted, but could be T2 or flair weighted.
* A lesion mask with values of 1 in the lesion and 0 elsewhere.
* See :ref:`Batch and Scripting <batch-scripts-spm>` for suggestions about file naming that will make it easier to script your resulting batch job.

Steps
*****

Coregister: Reslice Lesion Mask to TPM Space
==============================================
* The lesion mask must be in TPM space before it can be used to define the additional tissue type.
* Open Matlab (and optionally navigate to the relevant directory).
* Type *spm* at the Matlab command prompt. This will open spm
* Click the *fMRI* button which will open the windows you need.
* Select *Batch* and from the menubar: *SPM ➜ Spatial ➜ Coregister ➜ Coregister: Reslice*.

.. image:: /pictures/spm_anat_normalization-lesion-tpm_1.png
    :alt:  SPM12 Batch editor: From menu, select SPM->Spatial->Coregister->Coregister: Reslice

*	An **X** is displayed for the two parameters that must be specified: *Image Defining Space* and *Images to Reslice*.
* The *Image Defining Space* is the TPM.nii, typically found in the *spm12/tpm* directory.
* The *Images to Reslice* will be the lesion mask.
* Under *Interpolation* choose *Nearest neighbour* This will insure the lesion mask keeps mask values at or near 0 and 1.
* All other values should be left as their defaults.
* This is the first module of your batch job.

Segment: Estimate Warp Field
==============================

* From the batch editor choose: *SPM ➜ Spatial ➜ Segment*
*	Under *Volumes*, an **X** is displayed, indicating that this parameter must be specified. Specify the native space anatomical image that you used to draw the lesion.
* Click *Tissues* in the module options.
* Under *Current Items: Tissue*, click *New Tissue*.
* Scroll to the bottom of the tissue list, where you should find an **X** for *Tissue probability map*.
* Choose *Dependency* (red box). In the popup *Tissue Probability map* choose *Coregister: Reslice: Resliced Images* (blue box). This is how you refer to the resliced lesion map **r*** that you have not yet created.
*	Scroll down to the bottom of the module options, and set *Deformation Fields* to *Forward*. The *Forward* warp will be used to warp native space images into standard space.
* All other values should be left as their defaults.

.. image:: /pictures/spm_anat_normalization-lesion-tpm_2.png
    :alt: SPM12 Batch editor: From menu, select SPM->Spatial->Segment. Choose Dependency button (red rectangle, lower right) to choose output from the previous step, even though that has not yet been run

* This is the second module of your batch job.

Normalise: Apply the Warp Field to Lesion Mask
===============================================

#. From the batch editor choose: *SPM ➜ Spatial ➜ Normalise ➜ Normalise: Write*
#. Double click *Data*. *Deformation Field* and *Image to Write* now appear in the menu.
#. For *Deformation Field*, choose the *Dependency* button and specify *Segment: Forward deformations*
#. Under *Image to Write*, specify the native space lesion file that you want to warp.

* Under *Interpolation* choose *Nearest neighbour* This will ensure the lesion mask keeps mask values at or near 0 and 1.
* All other values should be left as their defaults.
* This is the third module of your batch job.

Normalise: Apply Warp Field to Brain and Head
==============================================

* You should apply the warp field to the original native space anatomical image as well. This is a sanity check because you can easily see inappropriate deformations of the whole head that you might not notice in the lesion file alone.
* Repeat the first four steps above to add a fourth batch module.
* Add the native space image for *Image to Write*.
* Use the default interpolation: *4th degree B-Spline*.
* All other values should be left as their defaults.
* This is the fourth module of your batch job.

Run Batch and View Results
===============================

* Run the batch module by clicking the green go button (upper left on batch editor).
* Reslicing produces a new lesion file prefixed with **r** to indicate it has been resliced.
* Segmentation produces:

  * Files prefixed with **c** for each tissue type and the skull.
  * A *seg8.mat* file containing segmentation parameters.
  * A deformation field image with **y** prepended.
  * If you elected to create an Inverse deformation as well, that will be prefixed with **iy**.

* Normalization produces:

  * A lesion image in standard MNI space. It has a **w** prefixed to the name to indicate that it has been warped.
  * An anatomical image in standard MNI space, also with a **w** prepended.