.. _spm_lesion_norm_old:

=====================================================
SPM Lesion Normalization with Source Weighting Image
=====================================================

| Maintainer: Dianne Patterson Ph.D. dkp @ arizona.edu
| Date Created: 2018_07_10
| 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 an inverse lesion mask to define areas that should influence the warp. The old normalize procedure did not depend on an initial segmentation and thus had distinct disadvantages over the newer registration that matches tissue type boundaries.

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.

Steps
*****

Create Inverse Lesion Mask
============================

If you have a mask with 1 anywhere there is lesion and 0 elsewhere, you need the inverse of that.
To create this inverse mask in SPM12, you can use the image calculator (N.B. Although the resulting mask displayed in FSL shows the "1" to be slightly more or less than 1, SPM nevertheless seems to treat the result as a true binary mask).  You have two choices for accessing the image calculator:

* Choose ImCalc from the main SPM menu

.. image:: /pictures/spm_anat_normalization-lesion-old_1.png
    :alt: SPM12 interface: ImCalc selected

* Select *Batch* and from the menubar: *SPM ➜ Util ➜ Image Calculator*

.. image:: /pictures/spm_anat_normalization-lesion-old_2.png
    :alt: SPM12 Batch editor: From menu, select SPM->Util->Image Calculator

*	An **X** is displayed for the two parameters that must be specified: *Input Images* and *Expression*. You may also change the Output filename and directory.
* The *Input Image* will be the native space lesion mask
* The expression will be **(i1 .* -1)+1**
* Set *Interpolation* to Nearest Neighbor to prevent values between 0 and 1 from being created at the edges of the lesion.
* Set *Data Type* to *UINT8 -unsigned char*

.. image:: /pictures/spm_anat_normalization-lesion-old_3.png
    :alt: SPM12 Batch editor for Image Calculator: Choose correct data type

* In the image calculator, *i1* always refers to the first input image you selected (i2= the second image etc.). In this expression we multiply all values in *i1* by -1, so 0 remains 0, but 1 becomes -1. This inverts the values.Then we add 1 to all voxels the resulting image so that the range is 0 to 1 and the values have been inverted.
* This is the first module of your batch.

Old Normalize: Estimate and Write Lesion Mask
==============================================

* Select *Batch* and from the menubar: *SPM ➜ Tools ➜ Old Normalise ➜ Old Normalise: Estimate and Write*
*	Click *Data*, and select *New Subject* from the grey *Current Item: Data* box below.  **X** values are displayed, indicating parameters that must be specified.
* Specify the native space anatomical image that you used to draw the lesion as the *Source Image*. * We also want a *Source Weighting Image*. Click *Source Weighting Image* and select the *Dependency* button. Choose the *Image Calculator: ImCalc Computed Image* for your inverse lesion file.
* For *Images to Write* select your original lesion file.
* Under *Estimation Options* Select a *Template Image* from the OldNorm subdirectory, choose a template with the same contrast as your source image (i.e., if our source image is a T1, choose T1.nii.)
* Under *Writing Options* find *Interpolation* and select *Nearest neighbour*

.. image:: /pictures/spm_anat_normalization-lesion-old_4.png
    :alt: SPM12 Batch editor: From menu, select SPM->Tools->Old Normalise->Old Normalise: Estimate & Write

* This is the second module of your batch.

Old Normalize: Write Anatomy file
==============================================

* From the batch editor, choose: *SPM ➜ Tools ➜ Old Normalise ➜ Old Normalise: Write*
* For the *Parameter file* select *Dependency* and the only *Norm Params File* available.
* Select the anatomical file for *Images to Write*
* Leave the default trilinear interpolation for this one.
* All other values should be left as their defaults.

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

* Run the batch module by clicking the green go button (upper left on batch editor).
* The ImCalc module will generate the inverse lesion mask.
* Normalization produces warped files prefixed with *w*.
* In addition, a *_sn.mat* file is produced that can be used to write additional warped images.