/DP_Milan_Nemy.pdf --- text of the masters thesis
/scripts --- all scripts used in the thesis
     .../bashScripts --- all scripts written in a Unix shell
          .../preprocess.sh --- preprocessing pipeline
	  .../create_template.sh --- creating the average group template
	  .../TemplateMultivariateBSplineSyN --- folder containing the average group template 
						 and some temporary files from each iteration 
						 of template construction
               .../T_template0.nii.gz --- average group template
     .../RScripts -- all scripts written in R language
          .../segment.r --- template segmentation into white matter, grey matter and CSF
	  .../stats01.r --- computation of statistical mapping between healthy and AD subjects
          .../stats02.r --- classifiers evaluation
	  .../segm00.nii.gz --- manual segmentation from ITK-SNAP
	  .../tbmad --- folder containing AD data and associated scripts
               .../getJacAD.r --- compute jacobian determinant fields
	       .../toPDF.r --- a short script for exporting jacobian determinant color map into PDF
               .../plotAD.pdf --- one randomly chosen jacobian determinant map overlayed over
				  the original image
	       .../dataAD --- source AD data
	       .../output --- output jacobian determinant maps
                    .../brain* -- output folder of a single subject
                         .../origResampled.nii.gz --- preprocessed original image
			 .../logJac.nii.gz --- log jacobian determinant (in the template space)
			 .../invJacOrig.nii.gz --- log jacobian determinant (in the original space)
	       .../template --- group template
	  .../tbmnc --- folder containing NC (normal control) data and associated scripts
               .../getJacNC.r --- compute jacobian determinant fields
	       .../dataNC --- source NC data
	       .../output --- output jacobian determinant maps
                    .../brain* -- output folder of a single subject
			 .../logJac.nii.gz --- log jacobian determinant (in the template space)
	       .../template --- group template

Remark: The provided data are only a testing sample. For the complete set feel free to contact the supervisor.
     
	  
