-
Notifications
You must be signed in to change notification settings - Fork 5
/
Contents.m
180 lines (177 loc) · 6.58 KB
/
Contents.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
% Computational Anatomy Toolbox
% Version 2620 (CAT12.9) 2024-10-11
% ______________________________________________________________________
%
% Christian Gaser, Robert Dahnke
% Structural Brain Mapping Group (https://neuro-jena.github.io)
% Departments of Neurology and Psychiatry
% Jena University Hospital
% ______________________________________________________________________
% $Id$
% ==========================================================================
% Description
% ==========================================================================
% This toolbox is a collection of extensions to the segmentation algorithm
% of SPM12 (Wellcome Department of Cognitive Neurology) to provide computational
% morphometry. It is developed by Christian Gaser and Robert Dahnke (Jena
% University Hospital, Departments of Psychiatry and Neurology) and is available
% to the scientific community under the terms of the GNU General Public Licence as
% published by the Free Software Foundation; either version 2 of the Licence,
% or (at your option) any later version.
%
% If you use any CAT12 code for commercial application, please email
% christian.gaser@uni-jena.de.
%
% General files
% INSTALL.txt - installation instructions
% CHANGES.txt - changes in revisions
% Contents.m - this file
%
% Core functions
% cat12.m
% cat_amap.m - compilation wrapper for cat_amap.c
% cat_main.m
% cat_run.m - runtime funtion for CAT12
% cat_run_job.m
% cat_run_newcatch.m
% cat_run_oldcatch.m
% cat_defaults.m - sets the defaults for CAT12
% cat_get_defaults.m - defaults for CAT12
% spm_cat12.m - toolbox wrapper to call CAT12
%
% Utilities
% cat_sanlm.m - Spatial Adaptive Non Local Means Denoising Filter
% cat_update.m - check for new updates
% cat_debug.m - print debug information for SPM12 and CAT12
% cat_ornlm.m
% cat_plot_boxplot.m
% slice_overlay.m - overlay tool
% sliderPanel.m
%
% Input & Output
% cat_io_3Dto4D.m
% cat_io_FreeSurfer.m
% cat_io_cgw2seg.m
% cat_io_checkinopt.m
% cat_io_cmd.m
% cat_io_colormaps.m
% cat_io_cprintf.m
% cat_io_csv.m
% cat_io_handle_pre.m
% cat_io_img2nii.m
% cat_io_matlabversion.m
% cat_io_remat.m
% cat_io_seg2cgw.m
% cat_io_struct2table.m
% cat_io_updateStruct.m
% cat_io_writenii.m
% cat_io_xml.m
% cat_io_xml2csv.m
%
% Longitudinal batch
% cat_long_main.m - longitudinal batch mode
% cat_long_multi_run.m - call cat_long_main for multiple subjects
%
% Statistics
% cat_stat_calc_stc.m
% cat_stat_homogeneity.m - check sample homogeneity across sample
% cat_stat_marks.m
% cat_stat_nanmean.m
% cat_stat_nanmedian.m
% cat_stat_nanstat1d.m
% cat_stat_nanstd.m
% cat_stat_nansum.m
% cat_stat_showslice_all.m - show 1 slice of all images
% cat_stat_spm.m
% cat_stat_spmF2x.m - transformation of F-maps to P, -log(P), R2 maps
% cat_stat_spmT2x.m - transformation of t-maps to P, -log(P), r or d-maps
% cat_stat_TIV.m - read total intracranial volume (TIV) from xml-files
%
% Surface functions
% cat_surf_avg.m
% cat_surf_calc.m
% cat_surf_createCS.m
% cat_surf_display.m
% cat_surf_info.m
% cat_surf_parameters.m
% cat_surf_rename.m
% cat_surf_render.m
% cat_surf_resamp.m
% cat_surf_resamp_freesurfer.m
% cat_surf_resample.m
% cat_surf_smooth.m
% cat_surf_vol2surf.m
%
% Test and experimental functions
% cat_tst_BWPsliceartifact.m
% cat_tst_CJV.m
% cat_tst_calc_kappa.m
% cat_tst_qa.m
% cat_tst_staple_multilabels.m
%
% Volume functions
% cat_vol_approx.m
% cat_vol_atlas.m
% cat_vol_average.m
% cat_vol_calc_roi.m
% cat_vol_correct_slice_scaling.m
% cat_vol_ctype.m
% cat_vol_defs.m - apply deformations to images
% cat_vol_findfiles.m
% cat_vol_groupwise_ls.m
% cat_vol_imcalc.m
% cat_vol_iscale.m
% cat_vol_morph.m - morphological operations to 3D data
% cat_vol_nanmean3.m
% cat_vol_partvol.m
% cat_vol_pbt.m
% cat_vol_resize.m
% cat_vol_sanlm.m - GUI for cat_sanlm
% cat_vol_series_align.m
% cat_vol_set_com.m
% cat_vol_slice_overlay.m - wrapper for overlay tool slice_overlay
% cat_vol_slice_overlay_ui.m - example for user interface for overlay wrapper cat_slice_overlay.m
% cat_vol_smooth3X.m
%
% Batch mode
% cat_batch_long.m - batch mode wrapper for spm_jobman for longitudinal pipeline
% cat_batch_spm.m - batch mode wrapper for spm_jobman for SPM12
% cat_batch_vbm.m - batch mode wrapper for spm_jobman for CAT12
%
% Check input and files
% cat_check.m
% cat_check_system_output.m
%
% Configuration
% cat_conf_extopts.m
% cat_conf_long.m
% cat_conf_opts.m
% cat_conf_stools.m
% cat_conf_stoolsexp.m
% cat_conf_tools.m - wrapper for calling CAT12 utilities
% tbx_cfg_cat.m
%
% Templates/Atlases volumes
% Template_?_GS.nii - Geodesic Shooting template of 555 subjects from IXI database
% in MNI152NLin2009cAsym space provided for 6 different iteration steps
% Template_T1.nii - average of 555 T1 images of IXI database in MNI152 space after
% Geodesic Shooting
% aal3.* - AAL3 atlas
% anatomy2.* - Anatomy2 atlas
% cobra.* - CoBra atlas
% hammers.* - Hammers atlas
% ibsr.* - IBSR atlas
% julichbrain.* _ JulichBrain atlas
% mori.* - Mori atlas
% thalamus.* - Thalamic Nuclei atlas
% neuromorphometrics.* - Neuromorphometrics atlas
% lpba40.nii - LPBA40 atlas
% brainmask.nii - brainmask
% cat12.nii - partitions for hemispheres, subcortical structures and vessels
%
% Templates/Atlases surfaces
% ?h.central.Template_T1.gii
% - central surface of Dartel average brain for result mapping
% ?h.central.freesurfer.gii - central surface of freesurfer fsaverage
% ?h.inflated.freesurfer.gii - inflated surface of freesurfer fsaverage
% ?h.sphere.freesurfer.gii - spherical surface of freesurfer fsvaverage