Removed files from LFS

ChristianGaser · Oct 16, 2023 · a7caafe · a7caafe
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Showing 45 changed files with 71 additions and 47 deletions.
diff --git 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
@@ -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
diff --git a/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii b/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii
diff --git a/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii b/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii
diff --git a/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii b/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii
diff --git a/templates_MNI152NLin2009cAsym/T1.nii b/templates_MNI152NLin2009cAsym/T1.nii
diff --git a/templates_MNI152NLin2009cAsym/TPM_Age11.5.nii b/templates_MNI152NLin2009cAsym/TPM_Age11.5.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_0_GS.nii b/templates_MNI152NLin2009cAsym/Template_0_GS.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii b/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_1_GS.nii b/templates_MNI152NLin2009cAsym/Template_1_GS.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii b/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_2_GS.nii b/templates_MNI152NLin2009cAsym/Template_2_GS.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_3_Dartel.nii b/templates_MNI152NLin2009cAsym/Template_3_Dartel.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_3_GS.nii b/templates_MNI152NLin2009cAsym/Template_3_GS.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_4_Dartel.nii b/templates_MNI152NLin2009cAsym/Template_4_Dartel.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_4_GS.nii b/templates_MNI152NLin2009cAsym/Template_4_GS.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii b/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii b/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_T1.nii b/templates_MNI152NLin2009cAsym/Template_T1.nii
diff --git a/templates_MNI152NLin2009cAsym/Template_T1_masked.nii b/templates_MNI152NLin2009cAsym/Template_T1_masked.nii
diff --git a/templates_MNI152NLin2009cAsym/Tian_Subcortex_S4_7T.nii b/templates_MNI152NLin2009cAsym/Tian_Subcortex_S4_7T.nii
diff --git a/templates_MNI152NLin2009cAsym/aal3.nii b/templates_MNI152NLin2009cAsym/aal3.nii
diff --git a/templates_MNI152NLin2009cAsym/anatomy3.nii b/templates_MNI152NLin2009cAsym/anatomy3.nii
diff --git a/templates_MNI152NLin2009cAsym/brainmask.nii b/templates_MNI152NLin2009cAsym/brainmask.nii
diff --git a/templates_MNI152NLin2009cAsym/brainmask_GM.nii b/templates_MNI152NLin2009cAsym/brainmask_GM.nii
diff --git a/templates_MNI152NLin2009cAsym/brainmask_GMtight.nii b/templates_MNI152NLin2009cAsym/brainmask_GMtight.nii
diff --git a/templates_MNI152NLin2009cAsym/brainmask_T1.nii b/templates_MNI152NLin2009cAsym/brainmask_T1.nii
diff --git a/templates_MNI152NLin2009cAsym/cat.nii b/templates_MNI152NLin2009cAsym/cat.nii
diff --git a/templates_MNI152NLin2009cAsym/cat_1mm.nii b/templates_MNI152NLin2009cAsym/cat_1mm.nii
diff --git a/templates_MNI152NLin2009cAsym/cat_bloodvessels.nii b/templates_MNI152NLin2009cAsym/cat_bloodvessels.nii
diff --git a/templates_MNI152NLin2009cAsym/cat_strokelesions_ATLAS303.nii b/templates_MNI152NLin2009cAsym/cat_strokelesions_ATLAS303.nii
diff --git a/templates_MNI152NLin2009cAsym/cat_wmh.nii b/templates_MNI152NLin2009cAsym/cat_wmh.nii
diff --git a/templates_MNI152NLin2009cAsym/cat_wmh_miccai2017.nii b/templates_MNI152NLin2009cAsym/cat_wmh_miccai2017.nii
diff --git a/templates_MNI152NLin2009cAsym/cobra.nii b/templates_MNI152NLin2009cAsym/cobra.nii
diff --git a/templates_MNI152NLin2009cAsym/hammers.nii b/templates_MNI152NLin2009cAsym/hammers.nii
diff --git a/templates_MNI152NLin2009cAsym/ibsr.nii b/templates_MNI152NLin2009cAsym/ibsr.nii
diff --git a/templates_MNI152NLin2009cAsym/julichbrain.nii b/templates_MNI152NLin2009cAsym/julichbrain.nii
diff --git a/templates_MNI152NLin2009cAsym/lpba40.nii b/templates_MNI152NLin2009cAsym/lpba40.nii
diff --git a/templates_MNI152NLin2009cAsym/mori.nii b/templates_MNI152NLin2009cAsym/mori.nii
diff --git a/templates_MNI152NLin2009cAsym/neuromorphometrics.nii b/templates_MNI152NLin2009cAsym/neuromorphometrics.nii
diff --git a/templates_MNI152NLin2009cAsym/suit.nii b/templates_MNI152NLin2009cAsym/suit.nii
diff --git 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
+--------------------------------------------------------------------------------
+$Id$
diff --git a/templates_MNI152NLin2009cAsym/thalamic_nuclei.nii b/templates_MNI152NLin2009cAsym/thalamic_nuclei.nii
diff --git a/templates_MNI152NLin2009cAsym/thalamus.nii b/templates_MNI152NLin2009cAsym/thalamus.nii