This toolbox is designed to help SPM12 normalize scans from indviduals with brain injury. For details visit the NITRC wiki
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 [email protected]: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);
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.
This software includes a BSD license
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.