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README.md

Clinical Toolbox for SPM

About

This toolbox is designed to help SPM12 normalize scans from indviduals with brain injury. For details visit the NITRC wiki

Installation

There are two ways to install this toolbox.

  • Click the green "Download or Clone" button, download as a zip file. Unzip the contents. Place the "Clinical" folder inside SPM12's "toolbox" folder. Restart SPM and press the "Batch" button. Use the Batch window's SPM/Tools/Clinical menu item to select the normalization you wish to compute. For more details see the included Word document or the Wiki listed above.
  • Run the following script in Matlab to install the software (assumes you have 'git' installed)
if isempty(which('spm')) || ~strcmp(spm('Ver'),'SPM12'), error('SPM12 required'); end;
pth = fullfile(spm('Dir'),'toolbox');
if ~exist(pth,'file'), error('SPM12 toolboxes not installed'); end;
cd(pth);
tbx = 'Clinical';
cmd = ['git clone git@github.com:neurolabusc', filesep, tbx, '.git'];
system(cmd);
pth = fullfile(pth, tbx);
if ~exist(pth,'file'), error('Unable to install toolbox'); end;
fprintf('Installed toolbox %s: to use launch SPM, choose "Batch" and select the SPM/Tools menu\n', tbx);
Recent Versions

9-May-2017

  • Automatic check for updates.
  • Compatibility fixes for SPM12
  • Segment-Normalize includes the ability to use 6-tissue segmentation maps (instead of 3 tissue segmentation maps). Requires SPM12. This is the new default, older 3-tissue is still available for compatibility.

7-July-2016

  • Enhanced support for SPM12 (SPM8 not tested still might work).
  • The command "MR segment-normalize" now includes the option for my implementation of enantiomorphic normalization (see Nachev et al., 2008). Users may also want to explore my script nii_enat_norm.
License

This software includes a BSD license

References

Nachev P, Coulthard E, Jäger HR, Kennard C, Husain M. (2008) Enantiomorphic normalization of focally lesioned brains. Neuroimage. 39(3):1215-26.

Rorden C, Bonilha L, Fridriksson J, Bender B, Karnath HO (2012) Age-specific CT and MRI templates for spatial normalization. NeuroImage. 61(4):957-65.

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