spm_auto_reorient_coregister : Cross-platform automatic AC-PC realignment/reorientation and coregistration robust to brain damage in SPM

This project is deprecated, please use the new one at: https://github.com/lrq3000/auto_acpc_reorient

Cross-platform automatic AC-PC realignment/reorientation and coregistration for both healthy volunteers and brain damaged patients using template matching in SPM 12.

This is a set of routines to perform "auto reorient" and "auto coregistration" in the toolbox Statistical Parametric Mapping 12 (SPM12).

Description

Setting up the AC-PC and reorienting images is a recurrent issue in between-subjects group analyses, since they rely on coregistration methods that, like the "unified segmentation" of SPM12, are for most sensitive to initial conditions (the starting orientation of the image). This routine is a somewhat enhanced version of the original code by John Ashburner.

The main function, spm_auto_reorient.m, automatically (but approximately) calculates a reorientation transform onto a target template in MNI space, in two steps: 1. a non-linear coregistration of the input image onto a target template in MNI space using spm_affreg is calculated, then another transform is calculated using Mutual Information on a joint histogram (spm_coreg), and then applies only the rigid-body transform part of both coregistrations to reorient the input image. This allows to mainly set the AC location and correct for head rotation and place the origin on AC, in order to further proceed with the segmentation/normalisation of the image. This relies on a "template matching" principle (as in the old normalize function), you therefore ought to specify the appropriate template/reference image (we provide some).

In any case, it is advised to check the automatically reoriented images, and fix the orientation manually (SPM -> Display) if necessary.

Another function, spm_auto_coreg.m, expands on the same ideas to allow coregistration between modalities (eg, between structural and functional). It is advised that spm_auto_reorient() to be first applied before applying spm_auto_coreg() (even if you do manually fix the reorientation, as this ensures that the T1 is somewhat in the MNI space, making it easier for spm_auto_coreg() to find the correct translation matrix).

Install

To install this tool :

• copy spm_auto_reorient.m and spm_auto_coreg.m in your spm folder. This will allow the command spm_auto_reorient() and spm_auto_coreg() to be called from command-line (if no argument is given, a file selector dialog will open).
• copy T1_template_CAT12_rm_withskull.nii to your spm/canonical folder. This is a template generated on 10 subjects using CAT12 that were manually reoriented to AC-PC and averaged, this provides better performance for reorientation than the more blurry MNI template. Note that this template is slightly better aligned to the AC-PC plane than the original MNI template, so that there may be a slight rotation bias compared to MNI if you use this custom template (usually it's mostly unnoticeable and this should have no influence if afterwards you do the SPM normalization on MNI on your data).
• Add spm12 and spm12\toolbox\OldNorm to the path in MATLAB.

The tool can be included in the batching system of SPM12 by :

• copying the spm_cfg_autoreorient.m file to the spm/config sub-directory. Then this module can be included in any processing pipeline;
• optionally, if you want an easy access from the SPM's spatial pull-down menu directly, by overwriting the spm_cfg.m with the one provided here (BEWARE: this was not updated since a long time, this may break down your SPM install!).

Usage

Type help spm_auto_reorient, for all the details and various options for reorientation of a T1.

Type help spm_auto_coreg for coregistering options.

Both scripts allows to use SPM filedialogs GUI, by simply typing spm_auto_reorient() or spm_auto_coreg in the MATLAB prompt.

General guideline:

• If you want to reorient isotropic T1, use spm_auto_reorient.
• If you want to reorient another modality (usually with less resolution), or an anisotropic T1, or an isotropic T1 but on your own custom T1 template, use spm_auto_coreg.

Guarantee

There is no guarantee that this will work 100% of the times, although it was observed to produce good results with our own data (young and old healthy subjects, AD/PD patients, most of brain damaged patients even with significant movement or metal artefacts).

The best results we got were by doing the following steps:

1. Call spm_auto_reorient() on the structural in MNI space, so that it is also matching other SPM templates
2. Manually review and fix the misoriented structural images
3. Coregister the functional to SPM12 EPI template (this allows a correct translation matrix and a good basis for rotation)
4. Coregister the functional onto the structural (this fine-tunes rotation to precisely match the subject's structural)

The last 2 steps can be done by calling spm_auto_coreg(), which has optimized default parameters for this task. For indication, on a dataset of 100 subjects with some heavily brain damaged or artifacted, the coregistration success rate was more than 95%.

For a comparison of various methods for AC-PC reorientation, the following article is a good read:

Liu, Yuan, and Benoit M. Dawant. "Automatic detection of the anterior and posterior commissures on MRI scans using regression forests." 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2014.

Citation

Please cite this work as following (a paper is in preparation but not available yet):

spm_auto_reorient_coregister RRID: SCR_017281. https://github.com/lrq3000/spm_auto_reorient_coregister

Authors

This software was developed by Stephen Karl Larroque (Coma Science Group, GIGA-Consciousness, University of Liege, Belgium).

The code is a fork from spm_auto_reorient (v1) written by Carlton Chu (FIL, UCL, London, UK) then modified and extended by Christophe Phillips (Cyclotron Research Centre, University of Liege, Belgium). It seems the very root of the code is from John Ashburner, although the history is unclear since no version control system was used for the initial release (so please excuse us if there is any inaccuracies and please let us know, we will happily update it).

Similar projects

We later found that K. Nemoto made a similar enhanced algorithm back in 2017, based on centering to the origin (instead of translating to match a template for us - what we call a pre-coregistration step) before applying the original auto_reorient.m script but tweaking it to apply a coregistration on a DARTEL template (instead of SPM12 ones in the original script, or a custom made template using CAT12 for this one). The resulting script, acpc_coreg.m, can be found on nemotos.net.

License

General Public License (GPL) v2.

Contact

For questions or suggestions, contact Stephen Karl Larroque at: stephen dot larroque at uliege dot be.