Shattuck DW, Sandor-Leahy SR, Schaper KA, Rottenberg DA, and Leahy RM, (2001) "Magnetic Resonance Image Tissue Classification Using a Partial Volume Model", Neuroimage 13(5):856-876 PMID: 11304082 S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004 PMID: 15501092 skullstrip fsl brainsuite bet http://pipeline.loni.ucla.edu/ hdr hdr pipeline://cranium.loni.usc.edu/LONI/data/Pipeline_Workflow_Test_Data/Training/raw_data.img hdr hdr pipeline://cranium.loni.usc.edu/{$tempdir}/pipelineTraining/{$username}/skullstrip_strict.img hdr hdr pipeline://cranium.loni.usc.edu/{$tempdir}/pipelineTraining/{$username}/skullstrip_tolerant.img Woods, R.P., Grafton, S.T., Holmes, C.J., Cherry, S.R., and Mazziotta, J.C. (1998a). Automated image registration: I. General methods and intrasubject, intramodality validation. J Comput Assist Tomogr V22, 139-152. PMID: 9448779 Woods, R.P., Grafton, S.T., Watson, J.D., Sicotte, N.L., and Mazziotta, J.C. (1998b). Automated image registration: II. Intersubject validation of linear and nonlinear models. J Comput Assist Tomogr 22, 153-165. PMID: 9448780 rotate mirror image http://bishopw.loni.ucla.edu/AIR5/reorient.html hdr hdr http://www.loni.ucla.edu/Software/license.php By registering for downloads from the UCLA Laboratory of Neuro Imaging, you are agreeing to the following terms and conditions as well as to the Terms of Use of the LONI website. To view the LONI website's Terms of Use go to, http://www.loni.ucla.edu/software/termsofuse.php. * Permission is granted to use this software without charge for non-commercial research purposes only. * Other than the rights granted herein, LONI retains all rights, title, and interest in LONI software and Technology, and You retain all rights, title, and interest in Your Modifications and associated specifications, subject to the terms of this License. * You may make verbatim copies of this software for personal use, or for use within your organization, provided that you duplicate all of the original copyright notices and associated disclaimers. If you provide the use of the software to other users within your organization, they also must comply with all the terms of this Software Distribution Agreement. * YOU MAY NOT DISTRIBUTE COPIES of this software, or copies of software derived from this software, to others outside your organization without specific prior written permission from the UCLA Laboratory of Neuro Imaging, except where noted for specific software products. * You must not remove or alter any copyright or other proprietary notices in the software. * Software has not been reviewed or approved by the Food and Drug Administration, and is for non-clinical, IRB-approved Research Use Only. In no event shall data or images generated through the use of the Software be used in the provision of patient care. * THE SOFTWARE IS PROVIDED "AS IS," AND THE UNIVERSITY OF CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE. * This software is for research purposes only and has not been approved for clinical use. * You may publish papers and books using results produced using software provided by this site provided that you reference the appropriate citations. A list of citations is available here. * You agree to comply with LONI's Trademark Usage Requirements, as modified from time to time, described in the "Use of Materials Limitations" section of the LONI Terms of Use Agreement. Except as expressly provided in this License, you are granted no rights in or to any LONI trademarks now or hereafter used or licensed by LONI. * All Technology and technical data delivered under this Agreement are subject to US export control laws and may be subject to export or import regulations in other countries. You agree to comply strictly with all such laws and regulations and acknowledge that you have the responsibility to obtain such licenses to export, re-export, or import as may be required after delivery to you. Shattuck DW, Sandor-Leahy SR, Schaper KA, Rottenberg DA, and Leahy RM, (2001) "Magnetic Resonance Image Tissue Classification Using a Partial Volume Model", Neuroimage 13(5):856-876 PMID: 11304082 skull stripping scalp removal http://www.loni.ucla.edu/~shattuck hdr hdr 0.62 10 3 0 1 2 0 hdr hdr hdr http://www.loni.ucla.edu/Software/license.php By registering for downloads from the UCLA Laboratory of Neuro Imaging, you are agreeing to the following terms and conditions as well as to the Terms of Use of the LONI website. To view the LONI website's Terms of Use go to, http://www.loni.ucla.edu/software/termsofuse.php. * Permission is granted to use this software without charge for non-commercial research purposes only. * Other than the rights granted herein, LONI retains all rights, title, and interest in LONI software and Technology, and You retain all rights, title, and interest in Your Modifications and associated specifications, subject to the terms of this License. * You may make verbatim copies of this software for personal use, or for use within your organization, provided that you duplicate all of the original copyright notices and associated disclaimers. If you provide the use of the software to other users within your organization, they also must comply with all the terms of this Software Distribution Agreement. * YOU MAY NOT DISTRIBUTE COPIES of this software, or copies of software derived from this software, to others outside your organization without specific prior written permission from the UCLA Laboratory of Neuro Imaging, except where noted for specific software products. * You must not remove or alter any copyright or other proprietary notices in the software. * Software has not been reviewed or approved by the Food and Drug Administration, and is for non-clinical, IRB-approved Research Use Only. In no event shall data or images generated through the use of the Software be used in the provision of patient care. * THE SOFTWARE IS PROVIDED "AS IS," AND THE UNIVERSITY OF CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE. * This software is for research purposes only and has not been approved for clinical use. * You may publish papers and books using results produced using software provided by this site provided that you reference the appropriate citations. A list of citations is available here. * You agree to comply with LONI's Trademark Usage Requirements, as modified from time to time, described in the "Use of Materials Limitations" section of the LONI Terms of Use Agreement. Except as expressly provided in this License, you are granted no rights in or to any LONI trademarks now or hereafter used or licensed by LONI. * All Technology and technical data delivered under this Agreement are subject to US export control laws and may be subject to export or import regulations in other countries. You agree to comply strictly with all such laws and regulations and acknowledge that you have the responsibility to obtain such licenses to export, re-export, or import as may be required after delivery to you. S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004 PMID: 15501092 skull stripping http://www.fmrib.ox.ac.uk/fsl/bet2/index.html hdr .nii.gz _mask.nii.gz .img .hdr _skull.img http://www.fmrib.ox.ac.uk/fsl/fsl/licence.html LICENCE FMRIB Software Library, Release 4.1 (c) 2008, The University of Oxford (the "Software") The Software remains the property of the University of Oxford ("the University"). The Software is distributed "AS IS" under this Licence solely for non-commercial use in the hope that it will be useful, but in order that the University as a charitable foundation protects its assets for the benefit of its educational and research purposes, the University makes clear that no condition is made or to be implied, nor is any warranty given or to be implied, as to the accuracy of the Software, or that it will be suitable for any particular purpose or for use under any specific conditions. Furthermore, the University disclaims all responsibility for the use which is made of the Software. It further disclaims any liability for the outcomes arising from using the Software. The Licensee agrees to indemnify the University and hold the University harmless from and against any and all claims, damages and liabilities asserted by third parties (including claims for negligence) which arise directly or indirectly from the use of the Software or the sale of any products based on the Software. No part of the Software may be reproduced, modified, transmitted or transferred in any form or by any means, electronic or mechanical, without the express permission of the University. The permission of the University is not required if the said reproduction, modification, transmission or transference is done without financial return, the conditions of this Licence are imposed upon the receiver of the product, and all original and amended source code is included in any transmitted product. You may be held legally responsible for any copyright infringement that is caused or encouraged by your failure to abide by these terms and conditions. You are not permitted under this Licence to use this Software commercially. Use for which any financial return is received shall be defined as commercial use, and includes (1) integration of all or part of the source code or the Software into a product for sale or license by or on behalf of Licensee to third parties or (2) use of the Software or any derivative of it for research with the final aim of developing software products for sale or license to a third party or (3) use of the Software or any derivative of it for research with the final aim of developing non-software products for sale or license to a third party, or (4) use of the Software to provide any service to an external organisation for which payment is received. If you are interested in using the Software commercially, please contact Isis Innovation Limited ("Isis"), the technology transfer company of the University, to negotiate a licence. Contact details are: innovation@isis.ox.ac.uk quoting reference BS/3497. S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004 PMID: 15501092 manipulation mathematical http://www.fmrib.ox.ac.uk/fsl/avwutils/index.html hdr 4D Noise Only AROC-thresh ROC ROC http://www.fmrib.ox.ac.uk/fsl/fsl/licence.html LICENCE FMRIB Software Library, Release 4.1 (c) 2008, The University of Oxford (the "Software") The Software remains the property of the University of Oxford ("the University"). The Software is distributed "AS IS" under this Licence solely for non-commercial use in the hope that it will be useful, but in order that the University as a charitable foundation protects its assets for the benefit of its educational and research purposes, the University makes clear that no condition is made or to be implied, nor is any warranty given or to be implied, as to the accuracy of the Software, or that it will be suitable for any particular purpose or for use under any specific conditions. Furthermore, the University disclaims all responsibility for the use which is made of the Software. It further disclaims any liability for the outcomes arising from using the Software. The Licensee agrees to indemnify the University and hold the University harmless from and against any and all claims, damages and liabilities asserted by third parties (including claims for negligence) which arise directly or indirectly from the use of the Software or the sale of any products based on the Software. No part of the Software may be reproduced, modified, transmitted or transferred in any form or by any means, electronic or mechanical, without the express permission of the University. The permission of the University is not required if the said reproduction, modification, transmission or transference is done without financial return, the conditions of this Licence are imposed upon the receiver of the product, and all original and amended source code is included in any transmitted product. You may be held legally responsible for any copyright infringement that is caused or encouraged by your failure to abide by these terms and conditions. You are not permitted under this Licence to use this Software commercially. Use for which any financial return is received shall be defined as commercial use, and includes (1) integration of all or part of the source code or the Software into a product for sale or license by or on behalf of Licensee to third parties or (2) use of the Software or any derivative of it for research with the final aim of developing software products for sale or license to a third party or (3) use of the Software or any derivative of it for research with the final aim of developing non-software products for sale or license to a third party, or (4) use of the Software to provide any service to an external organisation for which payment is received. If you are interested in using the Software commercially, please contact Isis Innovation Limited ("Isis"), the technology transfer company of the University, to negotiate a licence. Contact details are: innovation@isis.ox.ac.uk quoting reference BS/3497. S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004 PMID: 15501092 manipulation mathematical http://www.fmrib.ox.ac.uk/fsl/avwutils/index.html hdr 4D Noise Only AROC-thresh ROC ROC http://www.fmrib.ox.ac.uk/fsl/fsl/licence.html LICENCE FMRIB Software Library, Release 4.1 (c) 2008, The University of Oxford (the "Software") The Software remains the property of the University of Oxford ("the University"). The Software is distributed "AS IS" under this Licence solely for non-commercial use in the hope that it will be useful, but in order that the University as a charitable foundation protects its assets for the benefit of its educational and research purposes, the University makes clear that no condition is made or to be implied, nor is any warranty given or to be implied, as to the accuracy of the Software, or that it will be suitable for any particular purpose or for use under any specific conditions. Furthermore, the University disclaims all responsibility for the use which is made of the Software. It further disclaims any liability for the outcomes arising from using the Software. The Licensee agrees to indemnify the University and hold the University harmless from and against any and all claims, damages and liabilities asserted by third parties (including claims for negligence) which arise directly or indirectly from the use of the Software or the sale of any products based on the Software. No part of the Software may be reproduced, modified, transmitted or transferred in any form or by any means, electronic or mechanical, without the express permission of the University. The permission of the University is not required if the said reproduction, modification, transmission or transference is done without financial return, the conditions of this Licence are imposed upon the receiver of the product, and all original and amended source code is included in any transmitted product. You may be held legally responsible for any copyright infringement that is caused or encouraged by your failure to abide by these terms and conditions. You are not permitted under this Licence to use this Software commercially. Use for which any financial return is received shall be defined as commercial use, and includes (1) integration of all or part of the source code or the Software into a product for sale or license by or on behalf of Licensee to third parties or (2) use of the Software or any derivative of it for research with the final aim of developing software products for sale or license to a third party or (3) use of the Software or any derivative of it for research with the final aim of developing non-software products for sale or license to a third party, or (4) use of the Software to provide any service to an external organisation for which payment is received. If you are interested in using the Software commercially, please contact Isis Innovation Limited ("Isis"), the technology transfer company of the University, to negotiate a licence. Contact details are: innovation@isis.ox.ac.uk quoting reference BS/3497. pipeline://cranium.loni.usc.edu/smartline/Smartline.jar General hdr pipeline://cranium.loni.usc.edu/smartline/Smartline.jar General hdr