-
Notifications
You must be signed in to change notification settings - Fork 0
/
SAP_create_project.sh
237 lines (165 loc) · 11.8 KB
/
SAP_create_project.sh
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
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
#!/bin/bash
set -e
# Function: Create a directory hierarchy for a shape analysis project and place the subject T1 image files in the appropriate directory.
# NOTE: Can be done in Unix or Windows environment, but: 1) change paths to '/home/...' instead of '/c/...',
# and 2) change escape characters to LF (instead of CRLF) if executing in Unix (e.g., on P920).
########################################################################################################################################################################################################
# User defined variables
#PROJECT_DIR='/Windows/path/to/project/directory' # Choose directory in which to place the study
PROJECT_DIR='/Unix/path/to/project/directory' # P920 path
PROJECT="test" # Name the study/project
GROUP1='group1' # Name group 1
#GROUP2='cohort1_ses2' # Name group 2
#GROUP3='cohort1_ses3' # Name group 3
#GROUP4='cohort3_ses1' # Name group 4
#GROUP5='cohort5_ses1' # Name group 5
GROUP1_T1_RAW_DIR='/path/to/group1/T1/images' # Choose directory where raw T1 files for Group1 are located
#GROUP2_T1_RAW_DIR='/path/to/group2/T1/images' # Choose directory where raw T1 files for Group2 are located
#GROUP3_T1_RAW_DIR='/path/to/group3/T1/images' # Choose directory where raw T1 files for Group3 are located
#GROUP4_T1_RAW_DIR='/path/to/group4/T1/images' # Choose directory where raw T1 files for Group4 are located
#GROUP5_T1_RAW_DIR='/path/to/group5/T1/images' # Choose directory where raw T1 files for Group5 are located
########################################################################################################################################################################################################
echo -e "\n\n####################################################################################################"
echo -e "\nStarting program..."
echo -e "\n####################################################################################################"
########################################################################################################################################################################################################
# Create arrays for user-inputted variables
declare -a group_array # array for group names
declare -a t1_array # array for directories where raw T1 .nii files can be found
##################################################
# Group 1
if [[ -v GROUP1 ]] && [[ -v GROUP1_T1_RAW_DIR ]] && [[ -d $GROUP1_T1_RAW_DIR ]]; then
group_array=($GROUP1)
t1_array=($GROUP1_T1_RAW_DIR)
else
echo -e "\nNotice: Either the variable GROUP1 or the directory in which the original T1 files for GROUP1 are found hasn't been correctly specified. Please provide a group name and a T1 file directory, and run this program again."
exit 1
fi
##################################################
# Group 2
if [[ -v GROUP2 ]] && [[ -v GROUP2_T1_RAW_DIR ]] && [[ -d $GROUP2_T1_RAW_DIR ]]; then
group_array+=($GROUP2)
t1_array+=($GROUP2_T1_RAW_DIR)
else
echo -e "\nNotice: Either the variable GROUP2 or the directory in which the original T1 files for GROUP2 are found hasn't been correctly specified.\n"
read -p "Continue (y/n)? Answer: " choice
case "$choice" in
y|Y ) echo -e "\nConfirmed. Continuing program.";;
n|N ) echo -e "\nConfirmed. Exiting program."; exit 1;;
* ) echo -e "\nInvalid. Please type 'y' or 'n'. Exiting program."; exit 1;;
esac
fi
##################################################
# Group 3
if [[ -v GROUP3 ]] && [[ -v GROUP3_T1_RAW_DIR ]] && [[ -d $GROUP3_T1_RAW_DIR ]]; then
group_array+=($GROUP3)
t1_array+=($GROUP3_T1_RAW_DIR)
else
echo -e "\nNotice: Either the variable GROUP3 or the directory in which the original T1 files for GROUP3 are found hasn't been correctly specified.\n"
read -p "Continue (y/n)? Answer: " choice
case "$choice" in
y|Y ) echo -e "\nConfirmed. Continuing program.";;
n|N ) echo -e "\nConfirmed. Exiting program."; exit 1;;
* ) echo -e "\nInvalid. Please type 'y' or 'n'. Exiting program."; exit 1;;
esac
fi
##################################################
# Group 4
if [[ -v GROUP4 ]] && [[ -v GROUP4_T1_RAW_DIR ]] && [[ -d $GROUP4_T1_RAW_DIR ]]; then
group_array+=($GROUP4)
t1_array+=($GROUP4_T1_RAW_DIR)
else
echo -e "\nNotice: Either the variable GROUP4 or the directory in which the original T1 files for GROUP4 are found hasn't been correctly specified.\n"
read -p "Continue (y/n)? Answer: " choice
case "$choice" in
y|Y ) echo -e "\nConfirmed. Continuing program.";;
n|N ) echo -e "\nConfirmed. Exiting program."; exit 1;;
* ) echo -e "\nInvalid. Please type 'y' or 'n'. Exiting program."; exit 1;;
esac
fi
##################################################
# Group 5
if [[ -v GROUP5 ]] && [[ -v GROUP5_T1_RAW_DIR ]] && [[ -d $GROUP5_T1_RAW_DIR ]]; then
group_array+=($GROUP5)
t1_array+=($GROUP5_T1_RAW_DIR)
else
echo -e "\nNotice: Either the variable GROUP5 or the directory in which the original T1 files for GROUP5 are found hasn't been correctly specified.\n"
read -p "Continue (y/n)? Answer: " choice
case "$choice" in
y|Y ) echo -e "\nConfirmed. Continuing program.";;
n|N ) echo -e "\nConfirmed. Exiting program."; exit 1;;
* ) echo -e "\nInvalid. Please type 'y' or 'n'. Exiting program."; exit 1;;
esac
fi
########################################################################################################################################################################################################
# Check if group_array and t1_array are the same length (i.e. Every group has an associated T1 file directory). If not, exit the program.
echo ""
if [[ "${#group_array[@]}" -eq "${#t1_array[@]}" ]]; then
echo -e "\n##################################################"
echo -e "\nConfirmed: Every group has an associated raw T1 file directory from which to copy over the files. Continuing the program."
echo -e "\n##################################################"
#echo ${#group_array[@]}
else
echo -e "\n##################################################"
echo -e "\nERROR: There is a mismatch in the number of groups specified and the number of T1 file directories provided."
echo -e "\nEnsure that a T1 file directory is provided for every group, then run the program again. Exiting program."
exit 1
fi
########################################################################################################################################################################################################
# Create the project directory
if [[ ! -e $PROJECT_DIR ]]; then
echo -e "\n$PROJECT_DIR doesn't already exist. Creating the directory '$PROJECT_DIR' now."
mkdir -p $PROJECT_DIR/{T1_images,SPHARM_computation,population_analysis,covariate_significance,model2model_distance} # Create the project folder with all the required subfolders # Make PROJECT_DIR directory if it doesn't exist.
elif [[ ! -d $PROJECT_DIR ]]; then
echo -e "\n$PROJECT_DIR already exists but it is not a directory." 1>&2
exit 1
fi
########################################################################################################################################################################################################
# Create subdirectories for each group
echo -e "\n\n####################################################################################################"
echo -e "\nCreating project folder for $PROJECT_DIR..."
echo -e "\n####################################################################################################"
for i in ${group_array[@]}; do
echo -e "\n##################################################"
echo -e "Group: $i"
mkdir -p $PROJECT_DIR/T1_images/$i/masks_L/{hippo,lat_vent,insula} # Create GROUP_ folder + 'masks_L' folder in the T1_images subfolder (if previously specified and created)
mkdir -p $PROJECT_DIR/T1_images/$i/masks_R/{hippo,lat_vent,insula} # Create GROUP_ folder + 'masks_R' folder in the T1_images subfolder (if previously specified and created)
echo -e "\n$PROJECT_DIR/T1_images/$i/masks_L/ folder created."
echo -e "\n$PROJECT_DIR/T1_images/$i/masks_R/ folder created."
mkdir -p $PROJECT_DIR/SPHARM_computation/$i/masks_L/{SPHARM_vtk_models,ellalign_vtk_models,procalign_vtk_models,hippo,lat_vent,insula} # Create GROUP_ folder + 'masks_L' folder in the SPHARM_computation subfolder (if previously specified and created)
mkdir -p $PROJECT_DIR/SPHARM_computation/$i/masks_R/{SPHARM_vtk_models,ellalign_vtk_models,procalign_vtk_models,hippo,lat_vent,insula} # Create GROUP_ folder + 'masks_R' folder in the SPHARM_computation subfolder (if previously specified and created)
echo -e "\n$PROJECT_DIR/SPHARM_computation/$i/masks_L/ folder"
echo -e "\n$PROJECT_DIR/SPHARM_computation/$i/masks_R/ folder"
mkdir -p $PROJECT_DIR/covariate_significance/masks_L/{hippo,lat_vent,insula} # Create 'masks_L' folder + GROUP_ folder in the covariate_significance subfolder (if previously specified and created)
mkdir -p $PROJECT_DIR/covariate_significance/masks_R/{hippo,lat_vent,insula} # Create 'masks_R' folder + GROUP_ folder in the covariate_significance (if previously specified and created)
echo -e "\n$PROJECT_DIR/covariate_significance/masks_L/ folder created."
echo -e "\n$PROJECT_DIR/covariate_significance/masks_R/ folder created."
mkdir -p $PROJECT_DIR/population_analysis/masks_L/{hippo,lat_vent,insula} # Create 'masks_L' folder + GROUP_ folder in the population_analysis subfolder (if previously specified and created)
mkdir -p $PROJECT_DIR/population_analysis/masks_R/{hippo,lat_vent,insula} # Create 'masks_R' folder + GROUP_ folder in the population_analysis (if previously specified and created)
echo -e "\n$PROJECT_DIR/population_analysis/masks_L/ folder created."
echo -e "\n$PROJECT_DIR/population_analysis/masks_R/ folder created."
mkdir -p $PROJECT_DIR/model2model_distance/masks_L/{hippo,lat_vent,insula} # Create 'masks_L' folder + GROUP_ folder in the model2model_distance subfolder (if previously specified and created)
mkdir -p $PROJECT_DIR/model2model_distance/masks_R/{hippo,lat_vent,insula} # Create 'masks_R' folder + GROUP_ folder in the model2model_distance (if previously specified and created)
echo -e "\n$PROJECT_DIR/model2model_distance/masks_L/ folder created."
echo -e "\n$PROJECT_DIR/model2model_distance/masks_R/ folder created."
done
########################################################################################################################################################################################################
# Copy over T1 .nii scans for each group
echo -e "\n\n####################################################################################################"
echo -e "\nCopying all T1 .nii files to their respective directories..."
echo -e "\n####################################################################################################"
for i in ${!group_array[@]}; do
echo -e "\n##################################################"
echo -e "Group: ${group_array[$i]}"
cp -r ${t1_array[$i]}/* $PROJECT_DIR/T1_images/${group_array[$i]}
echo -e "\nAll T1 .nii files for ${group_array[$i]} were copied to directory $PROJECT_DIR/T1_images/${group_array[$i]}."
done
########################################################################################################################################################################################################
# Copy over template files
cp -r /k/UCLA_CBF_Project/template_files $PROJECT_DIR
########################################################################################################################################################################################################
# Program is complete
echo -e ""
echo -e "\n\####################################################################################################"
echo -e "\nNOTICE: The project directory hierarchy has been created."
echo -e "\n####################################################################################################"