Neurophysiological, imaging and neurobiological markers of central fatigue in multiple sclerosis.

1. #!/usr/bin/env bash
2. # Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
3. # This function warps an input volumes to a target volume space with specified ANTs warp or inverse warp files
5. ###########################################
6. # Main commands
7. ###########################################
8. main(){
10. # Set up warp files
11. warp=${warp_dir}/${warp_prefix}1Warp.nii.gz
12. inverse=${warp_dir}/${warp_prefix}1InverseWarp.nii.gz
13. affine=${warp_dir}/${warp_prefix}0GenericAffine.mat
15. # Set up fmri_reg command
16. if [ ! -z $fmri_reg ]; then
17. fmri_warp="-t $fmri_reg"
18. fi
20. # Set up time_series command
21. if [ $time_series -eq 1 ]; then
22. vol4d="-e 3"
23. fi
25. # Warp input volume to target's T1 space
26. output=$output_dir/${output_prefix}.nii.gz
27. if [ ! -e $output ]; then
28. case $warp_setting in
29. forward)
30. cmd="${ANTs_dir}/antsApplyTransforms -d 3 $vol4d -i $input -r $target -n $interp -t $warp -t $affine $fmri_warp"
31. cmd="$cmd -o $output"
32. echo $cmd
33. eval $cmd
34. ;;
35. inverse)
36. cmd="${ANTs_dir}/antsApplyTransforms -d 3 $vol4d -i $input -r $target -n $interp $fmri_warp -t [$affine, 1]"
37. cmd="$cmd -t $inverse -o $output"
38. echo $cmd
39. eval $cmd
40. ;;
41. *)
42. echo "Invalid warp setting. Use either 'forward' or 'inverse'"
43. esac
44. else
45. echo "The input volume have already been projected into ${target}'s space by ANTs"
46. fi
47. }
49. ##################################################################
50. # Function usage
51. ##################################################################
53. # Usage
54. usage() { echo "
55. Usage: CBIG_antsApplyReg_vol2vol.sh -i input -r target -w warp_prefix -p output_prefix
57. This script applies existing warps prepared using ANTs registration to map an input volume to a target volume.
59. REQUIRED ARGUMENTS:
61. -i <input> absolute path to input volume to map from
62. -r <target> absolute path to target volume to be mapped to
63. -w <warp_prefix> prefix of the warp files. Specifically, the affine, forward and inverse warps should have the
64. following names:
65. warp_prefix0GenericAffine.mat
66. warp_prefix1Warp.nii.gz
67. warp_prefix1InverseWarp.nii.gz
68. -p <output_prefix> prefix for output volume
70. OPTIONAL ARGUMENTS:
71. -f <fmri_reg> absolute path to native-to-T1 registration file for fMRI input. The file must have been
72. converted to format used by ANTs (e.g. .txt or .mat) if it was generated using other tools.
73. [ default: unset ]
74. -e <time_series> set this to 1 if the input volume is 4D (time-series)
75. [ default: 0 ]
76. -d <warp_dir> absolute path to the warps
77. [ default: $(pwd)/results ]
78. -o <output_dir> absolute path to output directory
79. [ default: $(pwd)/results ]
80. -s <warp setting> warping direction ('forward' for forward warp, 'inverse' for inverse warp). For example, if
81. the target space was registered to the input space during ANTs registration, then inverse
82. warp should be used to now map the input to the target.
83. [ default: forward ]
84. -t <interp> interpolation (Linear, NearestNeighbor, etc.)
85. [ default: Linear ]
86. -a <ANTs_dir> directory where ANTs is installed
87. [ default: $CBIG_ANTS_DIR ]
88. -h display help message
90. OUTPUTS:
91. $0 will create 1 output file in the output directory, corresponding to the input warped into target's space.
92. For example:
93. output_prefix.nii.gz
95. EXAMPLE:
96. $0 -i /path/to/my/data.nii.gz -r /path/to/my/template.nii.gz -w subject_moving_template_fixed -p data_to_template
97. -f data_to_T1.txt -s forward
99. " 1>&2; exit 1; }
101. # Display help message if no argument is supplied
102. if [ $# -eq 0 ]; then
103. usage; 1>&2; exit 1
104. fi
106. ##################################################################
107. # Assign input variables
108. ##################################################################
110. # Default parameter
111. warp_dir=$(pwd)/results
112. output_dir=$(pwd)/results
113. warp_setting=forward
114. interp=Linear
115. ANTs_dir=$CBIG_ANTS_DIR
116. time_series=0
118. # Assign parameter
119. while getopts "i:r:w:p:f:e:d:o:s:t:a:h" opt; do
120. case $opt in
121. i) input=${OPTARG} ;;
122. r) target=${OPTARG} ;;
123. w) warp_prefix=${OPTARG} ;;
124. p) output_prefix=${OPTARG} ;;
125. f) fmri_reg=${OPTARG} ;;
126. e) time_series=${OPTARG} ;;
127. d) warp_dir=${OPTARG} ;;
128. o) output_dir=${OPTARG} ;;
129. s) warp_setting=${OPTARG} ;;
130. t) interp=${OPTARG} ;;
131. a) ANTs_dir=${OPTARG} ;;
132. h) usage; exit ;;
133. *) usage; 1>&2; exit 1 ;;
134. esac
135. done
137. ##################################################################
138. # Check parameter
139. ##################################################################
141. if [ -z $target ]; then
142. echo "Reference volume not defined."; 1>&2; exit 1
143. fi
145. if [ -z $input ]; then
146. echo "Input volume not defined."; 1>&2; exit 1
147. fi
149. if [ -z $warp_prefix ]; then
150. echo "Warp prefix not defined."; 1>&2; exit 1
151. fi
153. if [ -z $output_prefix ]; then
154. echo "Output prefix not defined."; 1>&2; exit 1
155. fi
157. ##################################################################
158. # Disable multi-threading
159. ##################################################################
161. ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
162. export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
164. ##################################################################
165. # Set up output directory
166. ##################################################################
168. if [ ! -d "$output_dir" ]; then
169. echo "Output directory does not exist. Making directory now..."
170. mkdir -p $output_dir
171. fi
173. ###########################################
174. # Implementation
175. ###########################################
177. main

CBIG_antsApplyReg_vol2vol.sh at commit 35b5664, under MIT · at the source