SPM Lesion Normalization with Tissue Probability Maps

Maintainer: Dianne Patterson Ph.D. dkp @ email.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 Batch and Scripting 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.

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.

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

  1. From the batch editor choose: SPM ➜ Spatial ➜ Normalise ➜ Normalise: Write

  2. Double click Data. Deformation Field and Image to Write now appear in the menu.

  3. For Deformation Field, choose the Dependency button and specify Segment: Forward deformations

  4. 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.