diff --git a/.gitattributes b/.gitattributes index a732be6f..e96ef9ac 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,46 +1,3 @@ -templates_MNI152NLin2009cAsym/Template_T1.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Tian_Subcortex_S4_7T.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/cat_1mm.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Template_1_GS.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/cat_strokelesions_ATLAS303.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Template_4_Dartel.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Template_5_Dartel.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/thalamic_nuclei.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Template_2_Dartel.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/brainmask_GM.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/cat_wmh_miccai2017.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/thalamus.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/T1.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Template_6_Dartel.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Template_1_Dartel.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Template_3_Dartel.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/brainmask_T1.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/cat_bloodvessels.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/mori.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/lpba40.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Template_0_GS.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/aal3.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/cat_wmh.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/hammers.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/templates.man filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Template_T1_masked.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/ibsr.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/neuromorphometrics.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Template_3_GS.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/brainmask.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/cobra.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/julichbrain.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/TPM_Age11.5.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/brainmask_GMtight.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/cat.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/suit.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Template_2_GS.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/Template_4_GS.nii filter=lfs diff=lfs merge=lfs -text -templates_MNI152NLin2009cAsym/anatomy3.nii filter=lfs diff=lfs merge=lfs -text CAT.glnx86/CAT_SmoothConvexity filter=lfs diff=lfs merge=lfs -text CAT.glnx86/CAT_Surf2Sphere filter=lfs diff=lfs merge=lfs -text CAT.glnx86/CAT_FractalDimension filter=lfs diff=lfs merge=lfs -text diff --git a/cat_surf_vol2surf.m b/cat_surf_vol2surf.m index e6d4ad00..08491bbb 100644 --- a/cat_surf_vol2surf.m +++ b/cat_surf_vol2surf.m @@ -282,7 +282,7 @@ % with new template BB = spm_get_bbox(spm_vol(data_vol{vi})); if sum(sum(BB-[-90 -126 -72;90 90 108])) == 0 - fprintf('WARNING: File %s is not compatible to new template because a new MNI152NLin2009cAsym template space is used, which is not compatibe!\n',data_vol{vi}); + fprintf('WARNING: File %s is not compatible to new template because a new MNI152NLin2009cAsym template space is used, which is not compatible!\n',data_vol{vi}); end [ppv,ffv,eev] = spm_fileparts(data_vol{vi}); diff --git a/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii b/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii index 2cb9d904..a2144a1c 100644 Binary files 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a/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii b/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii index 2cccc075..edc331f7 100644 Binary files a/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii and b/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii differ diff --git a/templates_MNI152NLin2009cAsym/T1.nii b/templates_MNI152NLin2009cAsym/T1.nii index a3159f8d..b6bc1da6 100644 Binary files a/templates_MNI152NLin2009cAsym/T1.nii and b/templates_MNI152NLin2009cAsym/T1.nii differ diff --git a/templates_MNI152NLin2009cAsym/TPM_Age11.5.nii b/templates_MNI152NLin2009cAsym/TPM_Age11.5.nii index c28dd968..2dbb6632 100644 Binary files a/templates_MNI152NLin2009cAsym/TPM_Age11.5.nii and b/templates_MNI152NLin2009cAsym/TPM_Age11.5.nii differ diff --git a/templates_MNI152NLin2009cAsym/Template_0_GS.nii b/templates_MNI152NLin2009cAsym/Template_0_GS.nii index 92fc8a1c..bdd4409c 100644 Binary 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a/templates_MNI152NLin2009cAsym/templates.man b/templates_MNI152NLin2009cAsym/templates.man index 23be07bf..41979f5c 100644 --- a/templates_MNI152NLin2009cAsym/templates.man +++ b/templates_MNI152NLin2009cAsym/templates.man @@ -1,3 +1,70 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:7d4263ae05922c4d2b80e3d685a5226d376ff8d53ba494220631fd4f77c9cdcb -size 2697 +% Template_?_Dartel.nii +% --------------------------------- +% Dartel templates with 6 iteration steps +% +% This Dartel template was derived from 555 subjects from the IXI database: +% http://brain-development.org/ixi-dataset/ +% +% The Dartel toolbox was used to create the template and finally images +% were transformed to MNI152NLin2009cAsym space. +% +% Template_?_GS.nii +% --------------------------------- +% Geodesic shooting templates with 5 iteration steps +% +% This Geodesic Shooting template was derived from 555 subjects from the IXI +% database: +% http://brain-development.org/ixi-dataset/ +% +% The Geodesic Shooting toolbox was used to create the template and finally +% images were transformed to MNI152NLin2009cAsym space. +% +% Template_T1.nii +% --------------------------------- +% T1 in MNI152NLin2009cAsym space +% +% This is the MNI152NLin2009cAsym T1 template that can be used to overlay +% CAT12 results. +% +% Template_T1_masked.nii +% --------------------------------- +% Masked T1 in MNI152NLin2009cAsym space +% +% cat.nii +% --------------------------------- +% This is the CAT atlas where major anatomical structures are used for +% partitioning or for atlas based processing. Odd numbers code the left, even +% numbers the right hemisphere. In order to create this atlas several atlases +% such as AAL, Broadman, IXI, and Hammers atlas and the IBASPM toolbox +% (http://www.thomaskoenig.ch/Lester/ibaspm.htmAnatomy) were used. +% +% brainmask.nii +% ------------------------------ +% Image derived from average_305_mask_1mm.mnc, which was originally +% supplied by Alan Evans, MNI, Canada (ICBM, NIH P-20 project, +% Principal Investigator John Mazziotta). The original image +% contained ones and zeros, where ones represented voxels that were +% part of the brain. It was subsequently smoothed using an 8mm +% FWHM Gaussian. This volume can be used to weight the spatial +% normalisation so that the final solution is not influenced by +% voxels outside the brain. +% +% brainmask_T1.nii +% ------------------------------ +% Brainmask derived from segmentation of Template_T1.nii and thresholding +% the label image to obtain a brainmask for masking registered images in +% MNI152NLin2009cAsym space. +% +% brainmask_GM.nii +% ------------------------------ +% Brainmask for GM VBM analysis derived from Template_?_GS.nii which was +% smoothed with FWHM of 6mm and with the following thresholds: +% sGM > 0.25 & (sGM+sWM)>0.1 +% +% brainmask_GMtight.nii +% ------------------------------ +% A more tight brainmask for GM VBM analysis derived from Template_?_GS.nii +% with the following thresholds: +% GM > 0.2 & (GM+WM)>0.1 +-------------------------------------------------------------------------------- +$Id$ \ No newline at end of file diff --git a/templates_MNI152NLin2009cAsym/thalamic_nuclei.nii b/templates_MNI152NLin2009cAsym/thalamic_nuclei.nii index af0bccb8..a6920fae 100644 Binary files a/templates_MNI152NLin2009cAsym/thalamic_nuclei.nii and b/templates_MNI152NLin2009cAsym/thalamic_nuclei.nii differ diff --git a/templates_MNI152NLin2009cAsym/thalamus.nii b/templates_MNI152NLin2009cAsym/thalamus.nii index 78058b90..4f7f5b11 100644 Binary files a/templates_MNI152NLin2009cAsym/thalamus.nii and b/templates_MNI152NLin2009cAsym/thalamus.nii differ