Association between glymphatic dysfunction and glucose hypometabolism in chronic disorders of consciousness: a multimodal PET/MRI study.

1. #! /bin/bash
3. #############################################################
4. # Giuseppe Barisano - [email hidden]
5. #############################################################
7. ##### Computing diffusion along perivascular spaces (ALPS) from diffusion-weighted images #####
9. # REQUIRES: - FSL v. 6.0.3 or newer (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation)
10. # - MRtrix3 (https://www.mrtrix.org/download/)
11. # This script assumes that FSL and MRtrix3 are in your $PATH.
14. # initial directories and parameters
15. #script_folder="${ALPSDIR}"
16. script_folder="$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}"; )" &> /dev/null && pwd 2> /dev/null; )";
18. # inputs # 1 or 2 dwi files (if 2, they should be of opposite phase encoding direction, e.g., PA and AP)
19. # REQUIRED INPUTS
20. dwi1=''
21. bval1=''
22. bvec1=''
24. # Optional input for eddy current correction
25. json1='' # .json files with details about the diffusion sequence. Tested with .json files generated from dcm2niix https://github.com/rordenlab/dcm2niix)
27. # Optional second dwi inputs (needs to have opposite phase encoding direction and the first volume of both dwi1 and dwi2 must be a B0 image)
28. dwi2=''
29. bval2=''
30. bvec2=''
31. json2=''
33. # optional inputs with default options
34. denoise=1 # perform the denoise and unringing
35. rois=2.5 # perform the ROI analysis using the provided ROIs of 2.5 mm radius drawn on JHU-ICBM-FA-1mm.nii.gz
36. template=1 #use the FSL's JHU-ICBM-FA-1mm.nii.gz as FA template or FSL's MNI template if the structural MRI data is provided.
37. skip=0 #perform all the steps of the pipeline.
38. eddy=1 #try to use eddy_cpu
39. warp=0 #perform linear registration of the FA map to the template.
40. freg=1 #if the analysis is done on template space, by default it will use FSL's flirt or applywarp to transform the TENSOR file to the template.
41. struct='' #structural MRI data (can be either a T1-weighted or a T2-weighted image, no FLAIR, no PD)
42. weight=1 #if a structural MRI data is provided, by default it will be considered a T1-weighted image.
44. print_usage() {
45. printf "\nUsage: alps.sh \n\
46. -a DWI \n\
47. -b BVAL \n\
48. -c BVEC \n\
49. -m METADATA (.json file) \n\
50. -i DWI (second input with opposite phase encoding) \n\
51. -j BVAL of second input (MUST BE DEFINED if second dwi input -i is defined) \n\
52. -k BVEC of second input (MUST BE DEFINED if second dwi input -i is defined) \n\
53. -n METADATA (.json file) of second input (MUST BE DEFINED if second dwi input -i is defined) \n\
54. -d DENOISING \n\
55. -e EDDY (specify which eddy program to use)
56. -r ROIS \n\
57. -t TEMPLATE \n\
58. -v VOLUMETRIC structural MRI data \n\
59. -h WeigHt of the volumetric structural MRI data \n\
60. -w WARP the reconstructed FA map to the template \n\
61. -f Use flirt or applywarp or vecreg to transform the TENSOR file to the template \n\
62. -s SKIP preprocessing and DTI fitting, i.e. perform ONLY ROI analysis \n\
63. -o OUTPUT_DIR_NAME \n"
64. printf "\nDefault values: \n\
65. -d DENOISING [default = 1]; 0=skip; 1=both denoise and unringing; 2=only denoise; 3=only unringing. \n\
66. -e EDDY [default = 1]; 0=skip eddy (not recommended); 1=use ${FSLDIR}/bin/eddy_cpu; 2=use ${FSLDIR}/bin/eddy; 3=use ${FSLDIR}/bin/eddy_correct;
67. alternatively, the user can specify which eddy program to use (e.g., eddy_cuda). The binary file specified by the user must be located in ${FSLDIR}/bin/ (do not include \"${FSLDIR}/bin/\" in the command, just the name of the binary file)\n\
68. -r ROIS [default = 2.5]; 0=skip ROI analysis; 2.5=ROI analysis with provided ROIs drawn on JHU-ICBM-FA-1mm;
69. alternatively, a positive number (non-integer numbers are acceptable, e.g., 2.5) that is the radius of the new sphere ROIs that you want to use for ALPS calculation. They will be generated on the default FSL's JHU/MNI 1mm template space and will be available in the output folder.
70. alternatively, a comma-separated list of 4 custom ROI nifti files can be specified.
71. ROIs need to be in the following order: 1) LEFT and 2) RIGHT PROJECTION FIBERS (superior corona radiata), 3) LEFT and 4) RIGHT ASSOCIATION FIBERS (superior longitudinal fasciculus)\n\
72. -t TEMPLATE [default = 1]; 0=ROI analysis in NATIVE space; 1=ROI analysis with FSL's JHU-ICBM-FA-1mm (if no structural MRI data input), MNI_T1_1mm (if structural data input is a T1) or JHU-ICBM-T2-1mm (if structural data input is a T2); \n\
73. alternatively, the user can specify a template to use. \n\
74. -v VOLUMETRIC structural MRI data: specify a structural MRI data (a T1w or T2w NIFTI file) to be used for registration of the FA map to the template;
75. -h weight of the structural MRI data [default = 1]; 1=T1-weighted image; 2=T2-weighted image (no PD, no FLAIR).
76. -w WARP [default = 0]; 0=perform linear registration of the reconstructed FA map to the template; 1=perform ONLY non-linear registration (warping) of the reconstructed FA map to the template using FSL's suggested default parameters (not recommended). \n\
77. 2=perform linear (flirt) + non-linear registration (fnirt); option -w is ignored when a structural MRI is used (-v is not empty).
78. -f method to transform the TENSOR to the template [default = 1]; 1=use flirt (or applywarp if WARP is 1 or 2 or -V is not empty) to transform the TENSOR to the template; \n\
79. 2=use FSL's vecreg to transform the TENSOR to the template.
80. -s Option to skip preprocessing and DTI fitting, i.e. performs ONLY ROI analysis [default = 0]; 0 = all the steps are performed; 1= ONLY ROI analysis is performed;
81. If -s 1, then -o MUST BE DEFINED and MUST CORRESPOND TO THE FOLDER WHERE dxx.nii.gz, dyy.nii.gz and dzz.nii.gz ARE LOCATED. \n\
82. -o OUTPUT_DIR_NAME [default = 1]; default option will create a folder called \"alps\" located in the directory of the (first) input. \n\
83. \nExample with 1 input: sh alps.sh -a dwi.nii.gz -b id.bval -c id.bvec -m id.json -d 1 -o alps\n\
84. \nExample with 2 inputs with opposite phase encoding direction: sh alps.sh -a dwi_PA.nii.gz -b id_PA.bval -c id_PA.bvec -m id_PA.json -i dwi_AP.nii.gz -j id_AP.bval -k id_AP.bvec -n id_AP.json -d 1 -o alps\n"
85. }
87. while getopts 'a:b:c:m:i:j:k:n:d:e:r:t:v:h:w:f:s:o:' flag; do
88. case "${flag}" in
89. a) dwi1="$(echo "$(cd "$(dirname "${OPTARG}")" && pwd)/$(basename "${OPTARG}")")" ;;
90. b) bval1="$(echo "$(cd "$(dirname "${OPTARG}")" && pwd)/$(basename "${OPTARG}")")" ;;
91. c) bvec1="$(echo "$(cd "$(dirname "${OPTARG}")" && pwd)/$(basename "${OPTARG}")")" ;;
92. m) json1="$(echo "$(cd "$(dirname "${OPTARG}")" && pwd)/$(basename "${OPTARG}")")" ;;
93. i) dwi2="$(echo "$(cd "$(dirname "${OPTARG}")" && pwd)/$(basename "${OPTARG}")")" ;;
94. j) bval2="$(echo "$(cd "$(dirname "${OPTARG}")" && pwd)/$(basename "${OPTARG}")")" ;;
95. k) bvec2="$(echo "$(cd "$(dirname "${OPTARG}")" && pwd)/$(basename "${OPTARG}")")" ;;
96. n) json2="$(echo "$(cd "$(dirname "${OPTARG}")" && pwd)/$(basename "${OPTARG}")")" ;;
97. d) denoise="${OPTARG}" ;;
98. e) eddy="${OPTARG}" ;;
99. r) rois="${OPTARG}" ;;
100. t) template="${OPTARG}" ;;
101. v) struct="$(echo "$(cd "$(dirname "${OPTARG}")" && pwd)/$(basename "${OPTARG}")")" ;;
102. h) weight="${OPTARG}" ;;
103. w) warp="${OPTARG}" ;;
104. f) freg="${OPTARG}" ;;
105. s) skip="${OPTARG}" ;;
106. o) output_dir_name="${OPTARG}" ;;
107. *) print_usage
108. exit 1 ;;
109. esac
110. done
111. #INITIAL CHECKS
112. #INPUTS
113. if [ $skip -eq 0 ]; then #check the inputs only if are needed
114. if [ $OPTIND -eq 1 ]; then echo "ERROR! No options were passed"; print_usage; exit 1; fi
115. if [ ! $dwi1 ]; then echo "ERROR! input dwi (-a) is not defined."; print_usage; exit 1; fi
116. if [ ! $bval1 ]; then echo "ERROR! bval (-b) is not defined."; print_usage; exit 1; fi
117. if [ ! $bvec1 ]; then echo "ERROR! bvec (-c) is not defined."; print_usage; exit 1; fi
118. if [ ! -f "${dwi1}" ]; then echo "ERROR! input $dwi1 does not exist."; exit 1; fi
119. if [ ! -f "${bval1}" ]; then echo "ERROR! bval file $bval1 does not exist."; exit 1; fi
120. if [ ! -f "${bvec1}" ]; then echo "ERROR! bvec file $bvec1 does not exist."; exit 1; fi
121. #OUTPUT ALPS CHECK
122. if [ -f "${outdir}/alps.stat/alps.csv" ] && [ ! -z "`tail -n 1 "${outdir}/alps.stat/alps.csv" | tr -d ,`" ]; then echo "ERROR! Final output alps.csv already exists and is not empty! Remove/rename the output folder in order to re-run the pipeline with input $dwi1"; exit 1; fi;
123. # create output directory
124. if [ ! $output_dir_name ]; then
125. #study_folder="$(dirname "${dwi1}")"
126. study_folder=`echo "$(cd "$(dirname -- "${dwi1}")" >/dev/null; pwd -P)"`
127. outdir="${study_folder}/alps"
128. else
129. outdir="${output_dir_name}"
130. fi
131. echo "create output directory: ${outdir}"
132. mkdir -p "${outdir}"
133. #exec > "${outdir}"/alps_$(date +"%Y-%m-%d_%H-%M-%S")_log.txt 2>&1
134. exec > >(tee -a "${outdir}"/alps_$(date +"%Y-%m-%d_%H-%M-%S")_log.txt) 2> >(tee -a "${outdir}"/alps_$(date +"%Y-%m-%d_%H-%M-%S")_log.txt >&2)
136. #if [ ! $json1 ]; then echo "ERROR! metadata .json file (-m) is not defined."; print_usage; exit 1; fi
137. #CHECK FOR DWI2. Hashtagged, because:
138. #bvec2 is not used,
139. #bval2 might be skipped if the user verified that the first volume is a B0 volume
140. #json2 might be skipped if the user verified that the PE direction is opposite to that of dwi1.
141. #if [ $dwi2 ]; then if [ ! $bval2 ] || [ ! $bvec2 ] || [ ! $json2 ]; then echo "ERROR! dwi2 (-i) is defined, but bval (-j), bvec (-k), and/or metadata .json file (-n) of the second input is/are not defined."; print_usage; exit 1; fi; fi;
142. #if [ $bval2 ]; then if [ ! $dwi2 ] || [ ! $bvec2 ] || [ ! $json2 ]; then echo "ERROR! bval (-j) of the second input is defined, but dwi2 (-i), bvec (-k), and/or metadata .json file (-n) of the second input is/are not defined."; print_usage; exit 1; fi; fi;
143. #if [ $bvec2 ]; then if [ ! $dwi2 ] || [ ! $bval2 ] || [ ! $json2 ]; then echo "ERROR! bvec (-k) of the second input is defined, but dwi2 (-i), bval (-j), and/or metadata .json file (-n) of the second input is/are not defined."; print_usage; exit 1; fi; fi;
144. #if [ $json2 ]; then if [ ! $dwi2 ] || [ ! $bval2 ] || [ ! $bvec2 ]; then echo "ERROR! metadata .json file (-n) of the second input is defined, but dwi2 (-i), bval (-j), and/or bvec (-k) of the second input is/are not defined."; print_usage; exit 1; fi; fi;
145. if [ $dwi2 ]; then
146. if [ ! -f "${dwi2}" ]; then echo "ERROR! second input $dwi2 does not exist."; exit 1; fi;
147. #if [ $bval2 ]; then if [ ! -f "${bval2}" ]; then echo "ERROR! bval file $bval2 of second input does not exist."; exit 1; fi; fi;
148. #if [ ! -f "${bvec2}" ]; then echo "ERROR! bvec file $bvec2 of second input does not exist."; exit 1; fi;
149. #if [ $json2 ]; then if [ ! -f "${json2}" ]; then echo "ERROR! metadata .json file $json2 of second input does not exist."; exit 1; fi; fi;
150. fi
151. elif [ $skip -eq 1 ]; then
152. if [ ! $output_dir_name ]; then echo "ERROR! Option -s is set to 1, therefore option -o MUST BE DEFINED and MUST CORRESPOND TO THE FOLDER WHERE dxx.nii.gz, dyy.nii.gz and dzz.nii.gz ARE LOCATED."; exit 1; fi;
153. outdir="${output_dir_name}"
154. #exec > "${outdir}"/alps_$(date +"%Y-%m-%d_%H-%M-%S")_log.txt 2>&1
155. exec > >(tee -a "${outdir}"/alps_$(date +"%Y-%m-%d_%H-%M-%S")_log.txt) 2> >(tee -a "${outdir}"/alps_$(date +"%Y-%m-%d_%H-%M-%S")_log.txt >&2)
156. fi
157. #ROIS & TEMPLATE
158. if [ "$rois" != "0" ]; then
159. if [ "$rois" == "2.5" ]; then
160. echo "ROI analysis with default ROIs"
161. rois="${script_folder}/ROIs_JHU_ALPS/L_SCR.nii.gz,${script_folder}/ROIs_JHU_ALPS/R_SCR.nii.gz,${script_folder}/ROIs_JHU_ALPS/L_SLF.nii.gz,${script_folder}/ROIs_JHU_ALPS/R_SLF.nii.gz"
162. roption=$rois
163. elif [[ "$rois" =~ ^-?([0-9]+\.?[0-9]*|\.[0-9]+)$ ]]; then
164. radius=$rois
165. echo "ROI analysis with user-defined spheric ROIs with radius $radius mm"
166. rois="${script_folder}/ROIs_JHU_ALPS/L_SCR.nii.gz,${script_folder}/ROIs_JHU_ALPS/R_SCR.nii.gz,${script_folder}/ROIs_JHU_ALPS/L_SLF.nii.gz,${script_folder}/ROIs_JHU_ALPS/R_SLF.nii.gz" #only needed to pass the check below
167. roption=$radius
168. else
169. echo "ROI analysis with user-defined ROIs: $rois"
170. roption=$rois
171. fi
172. n_rois=`echo $rois | awk -F '[,]' '{print NF}'`
173. if [ $n_rois -ne 4 ]; then echo "ERROR! The number of ROIs is not equal to 4. The string of ROIs must include only 4 elements separated by 3 commas. Please double check that exactly 4 elements and no more than 3 commas are present in your string of ROIs (e.g., no commas is present in file/directory names."; exit 1; fi;
174. proj_L=`echo "$rois" | cut -d "," -f1`
175. proj_R=`echo "$rois" | cut -d "," -f2`
176. assoc_L=`echo "$rois" | cut -d "," -f3`
177. assoc_R=`echo "$rois" | cut -d "," -f4`
178. if [ ! -f "${proj_L}" ]; then echo "ERROR! Cannot find the following ROI file: ${proj_L}"; exit 1; fi;
179. if [ ! -f "${proj_R}" ]; then echo "ERROR! Cannot find the following ROI file: ${proj_R}"; exit 1; fi;
180. if [ ! -f "${assoc_L}" ]; then echo "ERROR! Cannot find the following ROI file: ${assoc_L}"; exit 1; fi;
181. if [ ! -f "${assoc_R}" ]; then echo "ERROR! Cannot find the following ROI file: ${assoc_R}"; exit 1; fi;
182. if [ "$template" != "0" ]; then #analysis in template space. Double check that the template exists.
183. #conditional for existence of structural MRI data.
184. if [ ! -z $struct ]; then
185. if [ ! -f "$struct" ]; then echo "ERROR! User specified to use $struct as structural MRI data, but I could not find it. Please double-check that the file exists."; exit 1; fi;
186. fi
187. #conditional for template selection
188. if [ "$template" == "1" ]; then
189. if [ -f ${FSLDIR}/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz ]; then
190. template_mask="--refmask=${FSLDIR}/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz "
191. #used only for fnirt (warp > 0 or !-z struct)
192. fi
193. if [ -z $struct ]; then
194. echo "Default FA template will be used: JHU-ICBM-FA-1mm.nii.gz"
195. template=${FSLDIR}/data/atlases/JHU/JHU-ICBM-FA-1mm.nii.gz
196. template_abbreviation=JHU-FA
197. elif [ ! -z $struct ]; then
198. if [ $weight == "1" ]; then
199. echo "The structural MRI $struct is a T1-weighted image, therefore the default template that will be used is: MNI152_T1_1mm"
200. template=${FSLDIR}/data/standard/MNI152_T1_1mm_brain.nii.gz
201. template_abbreviation=MNI152_T1_1mm
202. smri="t1w"
203. elif [ $weight == "2" ]; then
204. echo "The structural MRI $struct is a T2-weighted image, therefore the default template that will be used is: JHU-ICBM-T2-1mm"
205. template=${FSLDIR}/data/atlases/JHU/JHU-ICBM-T2-1mm.nii.gz
206. template_abbreviation=JHU-ICBM-T2-1mm
207. smri="t2w"
208. elif [ $weight -ne 1 ] && [ $weight -ne 2 ] && [ "$template" != "0" ] && [ "$template" != "1" ] ; then
209. echo "ERROR! A structural MRI data has been specified, but the user needs to specify with the option -h whether this is T1-weighted (-h 1) or T2-weighted (-h 2) in order to select a default template. \n\
210. The only allowed option for -h are 1 or 2. Alternatively, the user can specify the file template to use, and the option -h will be ignored."; exit 1;
211. fi
212. fi
213. else
214. template="$(echo "$(cd "$(dirname "${template}")" && pwd)/$(basename "${template}")")"
215. echo "User specified template: $template"
216. template_abbreviation=template
217. fi
218. if [ ! -f "${template}" ]; then echo "ERROR! Cannot find the template "$template". The template file must exist if -t option is not 0."; exit 1; fi;
219. if [ $warp -ne 0 ] && [ $warp -ne 1 ] && [ $warp -ne 2 ]; then echo "ERROR! The option specified with -w is $warp, which is not an allowed option. -w must be equal to 0 (for linear registration) or 1 (for non-linear registration)."; exit 1; fi;
220. if [ $freg -ne 1 ] && [ $freg -ne 2 ]; then echo "ERROR! The option specified with -f is $freg, which is not an allowed option. -f must be equal to 1 (for using FSL's flirt and/or applywarp depending on -w) or 2 (for using FSL's vecreg)."; exit 1; fi;
221. fi
222. fi
223. #OPTIONS
224. if [ "$denoise" != "0" ] && [ "$denoise" != "1" ] && [ "$denoise" != "2" ] && [ "$denoise" != "3" ]; then echo "-d option is equal to $denoise, which is not an allowed option. -d must be equal to 0, 1, 2, or 3, or skipped (which corresponds to -d 1)."; print_usage; exit 1; fi;
225. if [ "$eddy" == "1" ] && [ ! -f "${FSLDIR}/bin/eddy_cpu" ]; then echo "-e option (eddy) is equal to $eddy (default), which means using ${FSLDIR}/bin/eddy_cpu, but ${FSLDIR}/bin/eddy_cpu cannot be found. -e must be equal to 0 (skip eddy correction, not recommended) 1 (use ${FSLDIR}/bin/eddy_cpu), 2 (use ${FSLDIR}/bin/eddy), 3 (use ${FSLDIR}/bin/eddy_correct), or skipped (default value = 1). If the user wants to use a specific eddy program, this must be located in ${FSLDIR}/bin/"; print_usage; exit 1; fi;
226. if [ "$eddy" == "2" ] && [ ! -f "${FSLDIR}/bin/eddy" ]; then echo "-e option (eddy) is equal to $eddy (default), which means using ${FSLDIR}/bin/eddy, but ${FSLDIR}/bin/eddy cannot be found. -e must be equal to 0 (skip eddy correction, not recommended) 1 (use ${FSLDIR}/bin/eddy_cpu), 2 (use ${FSLDIR}/bin/eddy), 3 (use ${FSLDIR}/bin/eddy_correct), or skipped (default value = 1). If the user wants to use a specific eddy program, this must be located in ${FSLDIR}/bin/"; print_usage; exit 1; fi;
227. if [ "$eddy" == "3" ] && [ ! -f "${FSLDIR}/bin/eddy_correct" ]; then echo "-e option (eddy) is equal to $eddy (default), which means using ${FSLDIR}/bin/eddy_correct, but ${FSLDIR}/bin/eddy_correct cannot be found. -e must be equal to 0 (skip eddy correction, not recommended) 1 (use ${FSLDIR}/bin/eddy_cpu), 2 (use ${FSLDIR}/bin/eddy), 3 (use ${FSLDIR}/bin/eddy_correct), or skipped (default value = 1). If the user wants to use a specific eddy program, this must be located in ${FSLDIR}/bin/"; print_usage; exit 1; fi;
228. if [ "$eddy" != "0" ] && [ "$eddy" != "1" ] && [ "$eddy" != "2" ] && [ "$eddy" != "3" ] && [ ! -f "${FSLDIR}/bin/$eddy" ]; then echo "-e option (eddy) is equal to $eddy, but ${FSLDIR}/bin/$eddy cannot be found. -e must be equal to 0 (skip eddy correction, not recommended) or 1 (use eddy_cpu if available, or eddy if not), or skipped (default value = 1). If the user wants to use a specific eddy program, this must be located in ${FSLDIR}/bin/"; print_usage; exit 1; fi;
229. if [ "$skip" != "0" ] && [ "$skip" != "1" ]; then echo "-s option is equal to $skip, which is not an allowed option. -s must be equal to 0 or 1, or skipped (default value = 0)."; print_usage; exit 1; fi;
232. #running check
233. echo -e "Running ALPS with the following parameters: \n
234. -a $dwi1 \n
235. -b $bval1 \n
236. -c $bvec1 \n
237. -m $json1 \n
238. -i $dwi2 \n
239. -j $bval2 \n
240. -k $bvec2 \n
241. -n $json2 \n
242. -d $denoise \n
243. -e $eddy \n
244. -r $roption \n
245. -t $template \n
246. -v $struct \n
247. -h $weight \n
248. -w $warp \n
249. -f $freg \n
250. -s $skip \n
251. -o $output_dir_name"
254. # 1. PREPROCESSING (Denoising, unringing, Topup for Opposite EPI acquisitions, Eddy)
255. if [ $skip -eq 0 ]; then
257. #copy bval and bvec files into output directory
258. cp "$bvec1" "${outdir}/bvec1"
259. cp "$bval1" "${outdir}/bval1"
260. cd "${outdir}"
262. ## Denoising and/or unringing
263. if [ $denoise -ne 0 ]; then
264. if [ $denoise -eq 1 ]; then
265. echo "Denoising and unringing $dwi1"
266. dwidenoise "$dwi1" "${outdir}/dwi1.denoised.nii.gz"
267. mrdegibbs "${outdir}/dwi1.denoised.nii.gz" "${outdir}/dwi1.denoised.unring.nii.gz"
268. dwi1_processed="${outdir}/dwi1.denoised.unring.nii.gz"
269. fi
270. if [ $denoise -eq 2 ]; then
271. echo "Denoising $dwi1"
272. dwidenoise "$dwi1" "${outdir}/dwi1.denoised.nii.gz"
273. dwi1_processed="${outdir}/dwi1.denoised.nii.gz"
274. fi
275. if [ $denoise -eq 3 ]; then
276. echo "Unringing $dwi1"
277. mrdegibbs "$dwi1" "${outdir}/dwi1.unring.nii.gz"
278. dwi1_processed="${outdir}/dwi1.unring.nii.gz"
279. fi
280. else
281. echo "Denoising and unringing skipped by the user (-d 0 option)"
282. dwi1_processed="${dwi1}"
283. fi
285. # IF YOU HAVE A METADATA (JSON) FILE, THEN YOU CAN RUN EDDY with eddy_cpu
286. if [ -f "${json1}" ]; then
287. # ACQUISITION PARAMETERS OF FIRST INPUT (REQUIRED FOR EDDY)
288. #scanner1=$(jq -r '.Manufacturer' "$json1") # -r gives you the raw output
289. #scanner1=$(cat "${json1}" | grep -w Manufacturer | cut -d ' ' -f2 | tr -d ',')
290. scanner1=$(cat "${json1}" | awk -F'"' '/"Manufacturer"/ {print $4}')
291. if [[ "$scanner1" == *"Philips"* ]]
292. then
293. #PEdir1=$(jq -r '.PhaseEncodingAxis' "$json1")
294. #PEdir1=$(cat "${json1}" | grep -w PhaseEncodingAxis | cut -d ' ' -f2 | tr -d ',' | tr -d '"')
295. PEdir1=$(cat "${json1}" | awk -F'"' '/"PhaseEncodingAxis"/ {print $4}')
296. TotalReadoutTime1=0.1 #this assumes that the readout time is identical for all acquisitions on the Philips scanner. A "realistic" read-out time is ~50-100ms (and eddy accepts 10-200ms). So use 0.1 (i.e., 100 ms), not 1.
297. else
298. #PEdir1=$(jq -r '.PhaseEncodingDirection' "$json1")
299. #TotalReadoutTime1=$(jq -r '.TotalReadoutTime' "$json1")
300. #PEdir1=$(cat "${json1}" | grep -w PhaseEncodingDirection | cut -d ' ' -f2 | tr -d ',' | tr -d '"')
301. #TotalReadoutTime1=$(cat "${json1}" | grep -w TotalReadoutTime | cut -d ' ' -f2 | tr -d ',' | tr -d '"')
302. PEdir1=$(cat "${json1}" | awk -F'"' '/"PhaseEncodingDirection"/ {print $4}')
303. TotalReadoutTime1=$(cat "${json1}" | grep -w TotalReadoutTime | cut -d ':' -f2 | cut -d ',' -f1 | xargs)
305. fi
306. if [ "$PEdir1" = i ]; then printf "1 0 0 $TotalReadoutTime1" > "${outdir}/acqparams.txt";
307. elif [ "$PEdir1" = i- ]; then printf "-1 0 0 $TotalReadoutTime1" > "${outdir}/acqparams.txt";
308. elif [ "$PEdir1" = j ]; then printf "0 1 0 $TotalReadoutTime1" > "${outdir}/acqparams.txt";
309. elif [ "$PEdir1" = j- ]; then printf "0 -1 0 $TotalReadoutTime1" > "${outdir}/acqparams.txt";
310. elif [ "$PEdir1" = k ]; then printf "0 0 1 $TotalReadoutTime1" > "${outdir}/acqparams.txt";
311. elif [ "$PEdir1" = k- ]; then printf "0 0 -1 $TotalReadoutTime1" > "${outdir}/acqparams.txt";
312. fi
314. #IF YOU HAVE A SECOND DWI
315. if [ "$dwi2" ]; then
316. echo "2nd DWI is available"
317. #if [[ "$dwi2" == *".nii" ]]; then gzip "$dwi2"; fi
318. if [ $denoise -eq 1 ]; then
319. echo "Denoising and unringing $dwi2"
320. dwidenoise "$dwi2" "${outdir}/dwi2.denoised.nii.gz"
321. mrdegibbs "${outdir}/dwi2.denoised.nii.gz" "${outdir}/dwi2.denoised.unring.nii.gz"
322. dwi2_processed="${outdir}/dwi2.denoised.unring.nii.gz"
323. elif [ $denoise -eq 2 ]; then
324. echo "Denoising $dwi2"
325. dwidenoise "$dwi2" "${outdir}/dwi2.denoised.nii.gz"
326. dwi2_processed="${outdir}/dwi2.denoised.nii.gz"
327. elif [ $denoise -eq 3 ]; then
328. echo "Unringing $dwi2"
329. mrdegibbs "$dwi2" "${outdir}/dwi2.unring.nii.gz"
330. dwi2_processed="${outdir}/dwi2.unring.nii.gz"
331. elif [ $denoise -eq 0 ]; then
332. dwi2_processed="${dwi2}"
333. fi
335. ##
336. if [ "$json2" ]; then
337. #scanner2=$(jq -r '.Manufacturer' "$json2")
338. #scanner2=$(cat "${json2}" | grep -w Manufacturer | cut -d ' ' -f2 | tr -d ',')
339. scanner2=$(cat "${json2}" | awk -F'"' '/"Manufacturer"/ {print $4}')
340. if [[ "$scanner2" == *"Philips"* ]]
341. then
342. #PEdir2=$(jq -r '.PhaseEncodingAxis' "$json2")- #added "-" to make it opposite to the PEdir1. #Philips scans json files generated with dcm2niix have a problem where the PEdirection is the same (j) even though it is not.
343. #PEdir2=$(cat "${json2}" | grep -w PhaseEncodingAxis | cut -d ' ' -f2 | tr -d ',' | tr -d '"')
344. PEdir2=$(cat "${json2}" | awk -F'"' '/"PhaseEncodingAxis"/ {print $4}')
345. TotalReadoutTime2=0.1 #this assumes that the readout time is identical for all acquisitions on the Philips scanner. A "realistic" read-out time is ~50-100ms (and eddy accepts 10-200ms). So use 0.1 (i.e., 100 ms), not 1.
346. else
347. #PEdir2=$(jq -r '.PhaseEncodingDirection' "$json2")
348. #TotalReadoutTime2=$(jq -r '.TotalReadoutTime' "$json2")
349. #PEdir2=$(cat "${json2}" | grep -w PhaseEncodingDirection | cut -d ' ' -f2 | tr -d ',' | tr -d '"')
350. #TotalReadoutTime2=$(cat "${json2}" | grep -w TotalReadoutTime | cut -d ' ' -f2 | tr -d ',' | tr -d '"')
351. PEdir2=$(cat "${json2}" | awk -F'"' '/"PhaseEncodingDirection"/ {print $4}')
352. TotalReadoutTime2=$(cat "${json2}" | grep -w TotalReadoutTime | cut -d ':' -f2 | cut -d ',' -f1 | xargs)
353. fi
354. else #if you don't have a json2 file, then assume that the PEdir2 is opposite to PEdir1 and that the TotalReadoutTime2 is equal to TotalReadoutTime1
355. if [[ "${PEdir1}" == *"-"* ]]; then PEdir2=$(echo ${PEdir1} | tr -d '-')
356. else PEdir2="${PEdir1}-"
357. fi
358. TotalReadoutTime2=$TotalReadoutTime1
359. fi
361. # ACQUISITION PARAMETERS (ADDED TO THE PREVIOUS FILE)
362. if [ "$PEdir2" = i ]; then printf "\n1 0 0 $TotalReadoutTime2" >> "${outdir}/acqparams.txt";
363. elif [ "$PEdir2" = i- ]; then printf "\n-1 0 0 $TotalReadoutTime2" >> "${outdir}/acqparams.txt";
364. elif [ "$PEdir2" = j ]; then printf "\n0 1 0 $TotalReadoutTime2" >> "${outdir}/acqparams.txt";
365. elif [ "$PEdir2" = j- ]; then printf "\n0 -1 0 $TotalReadoutTime2" >> "${outdir}/acqparams.txt";
366. elif [ "$PEdir2" = k ]; then printf "\n0 0 1 $TotalReadoutTime2" >> "${outdir}/acqparams.txt";
367. elif [ "$PEdir2" = k- ]; then printf "\n0 0 -1 $TotalReadoutTime2" >> "${outdir}/acqparams.txt";
368. fi
371. #TOPUP (only if PEdir1 = PEdir2- and both DWI datasets have B0 images as first volume)
372. b0_dwi1=`head -c 1 "$bval1"`
373. if [ "$bval2" ]; then #if you don't have a bval2 file, then assume it equal to b0_dwi1, that should be 0.
374. b0_dwi2=`head -c 1 "$bval2"`
375. else
376. b0_dwi2=$b0_dwi1
377. fi
378. if [ "${PEdir1}" == "${PEdir2}-" ] || [ "${PEdir2}" == "${PEdir1}-" ] && ([ "${b0_dwi1}" == "${b0_dwi2}" ] && [ "${b0_dwi1}" == "0" ]);
379. then
380. b0_1="${outdir}/b0_first_direction.nii.gz"
381. b0_2="${outdir}/b0_second_direction.nii.gz"
382. fslroi "$dwi1_processed" "$b0_1" 0 1
383. fslroi "$dwi2_processed" "$b0_2" 0 1
385. #check dimensions of b0_1 and b0_2 because sometimes they are different and needs to be coregistered for fslmerge to work
386. dim1_1=`fslhd "$b0_1" | grep dim1 | tr -s ' ' | cut -d " " -f2 | head -n 1` #tr with the squeeze option makes all consecutive whitespaces equal to 1 whitespace
387. dim2_1=`fslhd "$b0_1" | grep dim2 | tr -s ' ' | cut -d " " -f2 | head -n 1` #tr with the squeeze option makes all consecutive whitespaces equal to 1 whitespace
388. dim3_1=`fslhd "$b0_1" | grep dim3 | tr -s ' ' | cut -d " " -f2 | head -n 1` #tr with the squeeze option makes all consecutive whitespaces equal to 1 whitespace
389. dim1_2=`fslhd "$b0_2" | grep dim1 | tr -s ' ' | cut -d " " -f2 | head -n 1` #tr with the squeeze option makes all consecutive whitespaces equal to 1 whitespace
390. dim2_2=`fslhd "$b0_2" | grep dim2 | tr -s ' ' | cut -d " " -f2 | head -n 1` #tr with the squeeze option makes all consecutive whitespaces equal to 1 whitespace
391. dim3_2=`fslhd "$b0_2" | grep dim3 | tr -s ' ' | cut -d " " -f2 | head -n 1` #tr with the squeeze option makes all consecutive whitespaces equal to 1 whitespace
392. if [ "${dim1_1}" != "${dim1_2}" ] || [ "${dim2_1}" != "${dim2_2}" ] || [ "${dim3_1}" != "${dim3_2}" ];
393. then
394. flirt -in "${b0_2}" -ref "${b0_1}" -out "${outdir}/b0_second_direction_reg" -omat "${outdir}/b0_2.in.b0_1.mat" -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 6
395. b0_2="${outdir}/b0_second_direction_reg.nii.gz"
396. echo "b0_2 registered to b0_1"
397. fi
399. fslmerge -t "${outdir}/both_b0" "$b0_1" "$b0_2"
400. temp=`fslhd "${dwi1}" | grep dim3`
401. dimtmp=( $temp )
402. n_slices=${dimtmp[1]}
403. echo "Running FSL TOPUP"
404. if [ $((n_slices%2)) -eq 0 ] #even number of slices
405. then
406. topup --imain=both_b0 --datain=acqparams.txt --config=b02b0.cnf --out=my_topup_results --iout=my_hifi_b0 #which will upon completion create the two files my_topup_results_fieldcoef.nii.gz (an estimate of the susceptibility induced off-resonance field), my_topup_results_movpar.txt and the non-distorted space my_hifi_b0.nii.gz
407. else #odd number of slices, use a different configuration file (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;6c4c9591.2002)
408. b02b0_1=`find /${FSLDIR} -name "b02b0_1.cnf" | head -n 1` #the location is usually ${FSLDIR}/src/topup/flirtsch/b02b0_1.cnf
409. if [ -z $b02b0_1 ]; then echo "ERROR! Could not find the configuration file required for running TOPUP on data with odd number of slices (your input has $n_slices slices). Should be in $FSLDIR."; exit 1;
410. else
411. topup --imain=both_b0 --datain=acqparams.txt --config=${b02b0_1} --out=my_topup_results --iout=my_hifi_b0 #which will upon completion create the two files my_topup_results_fieldcoef.nii.gz (an estimate of the susceptibility induced off-resonance field), my_topup_results_movpar.txt and the non-distorted space my_hifi_b0.nii.gz
412. fi
413. fi
414. # Processing of topup output
415. fslmaths my_hifi_b0 -Tmean my_hifi_b0
416. bet2 my_hifi_b0 b0_brain -m
418. #EDDY
419. if [ $eddy == "0" ]; then echo "EDDY skipped by the user (-e option is equal to $eddy)";
420. else
421. echo "Running EDDY with TOPUP RESULTS"
422. temp=`fslhd "${dwi1}" | grep dim4`
423. dimtmp=( $temp )
424. n_vol=${dimtmp[1]}
425. indx=""
426. for ((i=1; i<=$n_vol; i+=1)); do indx="$indx 1"; done
427. echo $indx > index.txt
428. if [ $eddy == "1" ] && [ -f ${FSLDIR}/bin/eddy_cpu ]; then
429. echo "Found eddy_cpu! Running ${FSLDIR}/bin/eddy_cpu with default options"
430. eddy_cpu --imain="$dwi1_processed" --mask=b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvec1 --bvals=bval1 --topup=my_topup_results --out=eddy_corrected_data
431. elif [ $eddy == "2" ] && [ -f ${FSLDIR}/bin/eddy ]; then
432. echo "Running ${FSLDIR}/bin/eddy with default options";
433. eddy --imain="$dwi1_processed" --mask=b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvec1 --bvals=bval1 --topup=my_topup_results --out=eddy_corrected_data
434. elif [ $eddy == "3" ] && [ -f ${FSLDIR}/bin/eddy_correct ]; then
435. echo "Running ${FSLDIR}/bin/eddy_correct with default options";
436. eddy_correct "$dwi1_processed" eddy_corrected_data 0 trilinear
437. else echo "Eddy with user-specified eddy program ${FSLDIR}/bin/$eddy"
438. "${FSLDIR}/bin/$eddy" --imain="$dwi1_processed" --mask=b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvec1 --bvals=bval1 --topup=my_topup_results --out=eddy_corrected_data
439. fi
440. fi
441. elif [ "${PEdir1}" != "${PEdir2}-" ] || [ "${PEdir2}" != "${PEdir1}-" ] || [ "${b0_dwi1}" != "${b0_dwi2}" ]; then
442. fslroi "$dwi1_processed" "${outdir}/b0" 0 1
443. bet2 "${outdir}/b0" "${outdir}/b0_brain" -m
444. #EDDY
445. if [ $eddy == "0" ]; then echo "EDDY skipped by the user (-e option is equal to $eddy)";
446. else
447. echo "Running EDDY (NO TOPUP) because PE directions are not opposite or b0 images are different"
448. temp=`fslhd "${dwi1}" | grep dim4`
449. dimtmp=( $temp )
450. n_vol=${dimtmp[1]}
451. indx=""
452. for ((i=1; i<=$n_vol; i+=1)); do indx="$indx 1"; done
453. echo $indx > index.txt
454. if [ $eddy == "1" ] && [ -f ${FSLDIR}/bin/eddy_cpu ]; then
455. echo "Found eddy_cpu! Running ${FSLDIR}/bin/eddy_cpu with default options"
456. eddy_cpu --imain="$dwi1_processed" --mask=b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvec1 --bvals=bval1 --out=eddy_corrected_data
457. elif [ $eddy == "2" ] && [ -f ${FSLDIR}/bin/eddy ]; then
458. echo "Running ${FSLDIR}/bin/eddy with default options";
459. eddy --imain="$dwi1_processed" --mask=b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvec1 --bvals=bval1 --out=eddy_corrected_data
460. elif [ $eddy == "3" ] && [ -f ${FSLDIR}/bin/eddy_correct ]; then
461. echo "Running ${FSLDIR}/bin/eddy_correct with default options";
462. eddy_correct "$dwi1_processed" eddy_corrected_data 0 trilinear
463. else echo "Eddy with user-specified eddy program ${FSLDIR}/bin/$eddy"
464. "${FSLDIR}/bin/$eddy" --imain="$dwi1_processed" --mask=b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvec1 --bvals=bval1 --out=eddy_corrected_data
465. fi
466. fi
467. fi
468. elif [ ! "$dwi2" ]; then
469. fslroi "$dwi1_processed" "${outdir}/b0" 0 1
470. bet2 "${outdir}/b0" "${outdir}/b0_brain" -m
471. #EDDY
472. if [ $eddy == "0" ]; then echo "EDDY skipped by the user (-e option is equal to $eddy)";
473. else
474. echo "Running EDDY only (NO TOPUP) because there is no dwi2"
475. temp=`fslhd "${dwi1}" | grep dim4`
476. dimtmp=( $temp )
477. n_vol=${dimtmp[1]}
478. indx=""
479. for ((i=1; i<=$n_vol; i+=1)); do indx="$indx 1"; done
480. echo $indx > index.txt
481. if [ $eddy == "1" ] && [ -f ${FSLDIR}/bin/eddy_cpu ]; then
482. echo "Found eddy_cpu! Running ${FSLDIR}/bin/eddy_cpu with default options"
483. eddy_cpu --imain="$dwi1_processed" --mask=b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvec1 --bvals=bval1 --out=eddy_corrected_data
484. elif [ $eddy == "2" ] && [ -f ${FSLDIR}/bin/eddy ]; then
485. echo "Running ${FSLDIR}/bin/eddy with default options";
486. eddy --imain="$dwi1_processed" --mask=b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvec1 --bvals=bval1 --out=eddy_corrected_data
487. elif [ $eddy == "3" ] && [ -f ${FSLDIR}/bin/eddy_correct ]; then
488. echo "Running ${FSLDIR}/bin/eddy_correct with default options";
489. eddy_correct "$dwi1_processed" eddy_corrected_data 0 trilinear
490. else echo "Eddy with user-specified eddy program ${FSLDIR}/bin/$eddy"
491. "${FSLDIR}/bin/$eddy" --imain="$dwi1_processed" --mask=b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvec1 --bvals=bval1 --out=eddy_corrected_data
492. fi
493. fi
494. fi
495. elif [ ! -f "${json1}" ] && [ $eddy == "3" ]; then
496. echo "Running ${FSLDIR}/bin/eddy_correct with default options";
497. eddy_correct "$dwi1_processed" eddy_corrected_data 0 trilinear
498. fi
501. # 2. FIT TENSOR
502. if [ -f "${outdir}/eddy_corrected_data.nii.gz" ]; then
503. echo "starting DTI FITTING on eddy corrected data"
504. if [ -f "${outdir}/eddy_corrected_data.eddy_rotated_bvecs" ]; then
505. echo "Using eddy_rotated_bvecs"
506. dtifit --data=eddy_corrected_data.nii.gz --out=dti --mask=b0_brain_mask.nii.gz --bvecs=eddy_corrected_data.eddy_rotated_bvecs --bvals=bval1 --save_tensor
507. else
508. dtifit --data=eddy_corrected_data.nii.gz --out=dti --mask=b0_brain_mask.nii.gz --bvecs=bvec1 --bvals=bval1 --save_tensor
509. fi
510. else
511. if [ -f "${dwi1_processed}" ]; then
512. fslroi "$dwi1_processed" "${outdir}/b0" 0 1
513. bet2 "${outdir}/b0" "${outdir}/b0_brain" -m
514. echo "starting DTI FITTING on preprocessed diffusion data (denoised and/or unringed, NO TOPUP, NO eddy correction)"
515. dtifit --data="${dwi1_processed}" --out=dti --mask=b0_brain_mask.nii.gz --bvecs=bvec1 --bvals=bval1 --save_tensor
516. else
517. fslroi "$dwi1" "${outdir}/b0" 0 1
518. bet2 "${outdir}/b0" "${outdir}/b0_brain" -m
519. echo "starting DTI FITTING on input diffusion data (NO preprocessing (denoising/unringing), NO TOPUP, NO eddy correction)"
520. dtifit --data="${dwi1}" --out=dti --mask=b0_brain_mask.nii.gz --bvecs=bvec1 --bvals=bval1 --save_tensor
521. fi
522. fi
524. echo "DTI FITTING completed!"
525. #fslsplit "${outdir}/dti_tensor.nii.gz"
526. #cp "${outdir}/vol0000.nii.gz" "${outdir}/dxx.nii.gz"
527. #cp "${outdir}/vol0003.nii.gz" "${outdir}/dyy.nii.gz"
528. #cp "${outdir}/vol0005.nii.gz" "${outdir}/dzz.nii.gz"
529. elif [ $skip -eq 1 ]; then
530. echo "Preprocessing and DTI fitting skipped by the user (-s 1 option). ONLY ROI ANALYSIS IS PERFORMED. Checking all required inputs are available..."
531. if [ -f "${outdir}/alps.stat/alps.csv" ] && [ ! -z "`tail -n 1 "${outdir}/alps.stat/alps.csv" | tr -d ,`" ]; then echo "ERROR! Final output alps.csv already exists and is not empty! Remove/rename the "alps.stat" folder or the "alps.stat/alps.csv" file in order to run the ROI analysis only (-s 1) in ${outdir}"; exit 1; fi;
532. if [ -f "${outdir}/dti_FA.nii.gz" ]; then echo "dti_FA.nii.gz is available for ROI analysis"; else echo "ERROR! Cannot find ${outdir}/dti_FA.nii.gz, needed for ROI analysis. Double check that ${outdir}/dti_FA.nii.gz exists; if it does not exist, consider running the whole alps script (-s 0, default option)"; exit 1; fi
533. if [ -f "${outdir}/dti_tensor.nii.gz" ]; then echo "dti_tensor.nii.gz is available for ROI analysis"; else echo "ERROR! Cannot find ${outdir}/dti_tensor.nii.gz, needed for ROI analysis. Double check that ${outdir}/dti_tensor.nii.gz exists; if it does not exist, consider running the whole alps script (-s 0, default option)"; exit 1; fi
534. #if [ -f "${outdir}/dxx.nii.gz" ]; then echo "dxx.nii.gz is available for ROI analysis"; else echo "ERROR! Cannot find ${outdir}/dxx.nii.gz, needed for ROI analysis. Double check that ${outdir}/dxx.nii.gz exists; if it does not exist, consider running the whole alps script (-s 0, default option)"; exit 1; fi
535. #if [ -f "${outdir}/dyy.nii.gz" ]; then echo "dyy.nii.gz is available for ROI analysis"; else echo "ERROR! Cannot find ${outdir}/dyy.nii.gz, needed for ROI analysis. Double check that ${outdir}/dyy.nii.gz exists; if it does not exist, consider running the whole alps script (-s 0, default option)"; exit 1; fi
536. #if [ -f "${outdir}/dyy.nii.gz" ]; then echo "dzz.nii.gz is available for ROI analysis"; else echo "ERROR! Cannot find ${outdir}/dzz.nii.gz, needed for ROI analysis. Double check that ${outdir}/dzz.nii.gz exists; if it does not exist, consider running the whole alps script (-s 0, default option)"; exit 1; fi
537. fi
539. # 3. ROI ANALYSIS
540. if [ "$rois" != "0" ]
541. then
542. if [ -z $radius ]; then
543. iteration=0
544. for r in $(echo $rois | tr -s ',' ' '); do
545. iteration=$((iteration+1))
546. cp "$r" "${outdir}/"$(basename "$(basename "$r" .gz)" .nii)"_in_${template_abbreviation}.nii.gz";
547. if [ $iteration -eq 1 ]; then
548. cp "${outdir}/"$(basename "$(basename "$r" .gz)" .nii)"_in_${template_abbreviation}.nii.gz" "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
549. else
550. fslmaths "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz" -add "${outdir}/"$(basename "$(basename "$r" .gz)" .nii)"_in_${template_abbreviation}.nii.gz" "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
551. fi
552. done
553. cluster -t 1 -i "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz" -o "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
554. #cp "${script_folder}/ROIs_JHU_ALPS/all_ROIs.nii.gz" "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
555. else #generate spheric ROIs in template space
556. if [ "${template}" == "0" ]; then template_roi=${FSLDIR}/data/atlases/JHU/JHU-ICBM-FA-1mm.nii.gz; template_abbreviation=JHU-FA; else template_roi="${template}"; fi
557. fslmaths "${template_roi}" -mul 0 -add 1 -roi 116 1 110 1 99 1 0 1 -kernel sphere $radius -fmean -bin "${outdir}/L_SCR_in_${template_abbreviation}.nii.gz" -odt float
558. fslmaths "${template_roi}" -mul 0 -add 1 -roi 64 1 110 1 99 1 0 1 -kernel sphere $radius -fmean -bin "${outdir}/R_SCR_in_${template_abbreviation}.nii.gz" -odt float
559. fslmaths "${template_roi}" -mul 0 -add 1 -roi 128 1 110 1 99 1 0 1 -kernel sphere $radius -fmean -bin "${outdir}/L_SLF_in_${template_abbreviation}.nii.gz" -odt float
560. fslmaths "${template_roi}" -mul 0 -add 1 -roi 52 1 110 1 99 1 0 1 -kernel sphere $radius -fmean -bin "${outdir}/R_SLF_in_${template_abbreviation}.nii.gz" -odt float
561. fslmaths "${outdir}/L_SCR_in_${template_abbreviation}.nii.gz" -add "${outdir}/R_SCR_in_${template_abbreviation}.nii.gz" -add "${outdir}/L_SLF_in_${template_abbreviation}.nii.gz" -add "${outdir}/R_SLF_in_${template_abbreviation}.nii.gz" -bin "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
562. cluster -t 1 -i "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz" -o "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
563. fi
564. rois="${outdir}/L_SCR_in_${template_abbreviation}.nii.gz","${outdir}/R_SCR_in_${template_abbreviation}.nii.gz","${outdir}/L_SLF_in_${template_abbreviation}.nii.gz","${outdir}/R_SLF_in_${template_abbreviation}.nii.gz"
565. proj_L="${outdir}/L_SCR_in_${template_abbreviation}.nii.gz"
566. proj_R="${outdir}/R_SCR_in_${template_abbreviation}.nii.gz"
567. assoc_L="${outdir}/L_SLF_in_${template_abbreviation}.nii.gz"
568. assoc_R="${outdir}/R_SLF_in_${template_abbreviation}.nii.gz"
569. #ROIs
570. echo "starting ROI analysis with projection fibers "$(basename "$proj_L")" (LEFT) and "$(basename "$proj_R")" (RIGHT), and association fibers "$(basename "$assoc_L")" (LEFT) and "$(basename "$assoc_R")" (RIGHT)"
571. #TEMPLATE
572. if [ "$template" != "0" ]; then #analysis in template space
573. if [ -f "$struct" ]; then #if you have structural MRI data
574. echo "Linear (flirt) + Non-Linear (fnirt) registration to template via structural scan";
575. cp "$struct" "${outdir}/${smri}.nii.gz"
576. #hashtagged the following 2 lines because bet2 does not work super well in all struct MRI scans.
577. #bet2 "${outdir}/${smri}.nii.gz" "${outdir}/${smri}_brain" -m #this is used for flirt dti2struct and flirt struct2template
578. #flirt -ref "${outdir}/${smri}_brain.nii.gz" -in "${outdir}/dti_FA.nii.gz" -dof 6 -omat "${outdir}/dti2struct.mat"
579. if [ $weight == "1" ]; then
580. flirt -ref "${outdir}/${smri}.nii.gz" -in "${outdir}/dti_FA.nii.gz" -dof 6 -out "${outdir}/dti_FA_2_${smri}.nii.gz" -omat "${outdir}/dti2struct.mat"
581. elif [ $weight == "2" ]; then #if it's a T2, it's better to align the b0 volume rather than the FA, because the b0 contrast is more similar to T2.
582. if [ -f "${outdir}/b0.nii.gz" ]; then
583. flirt -ref "${outdir}/${smri}.nii.gz" -in "${outdir}/b0.nii.gz" -dof 6 -out "${outdir}/b0_2_${smri}.nii.gz" -omat "${outdir}/dti2struct.mat"
584. else #in case you don't have b0 (i.e., you skipped the preprocessing, and are only doing ROI analysis with a dti_FA map ready)
585. flirt -ref "${outdir}/${smri}.nii.gz" -in "${outdir}/dti_FA.nii.gz" -dof 6 -out "${outdir}/dti_FA_2_${smri}.nii.gz" -omat "${outdir}/dti2struct.mat"
586. fi
587. fi
588. if [ -f "${outdir}/b0_brain_mask.nii.gz" ]; then
589. flirt -in "${outdir}/b0_brain_mask.nii.gz" -ref "${outdir}/${smri}.nii.gz" -interp nearestneighbour -out "${outdir}/b0_brain_mask_2_struct.nii.gz" -init "${outdir}/dti2struct.mat" -applyxfm
590. fslmaths "${outdir}/${smri}.nii.gz" -mul "${outdir}/b0_brain_mask_2_struct.nii.gz" "${outdir}/${smri}_brain.nii.gz"
591. else #in case you don't have b0_brain_mask (i.e., you skipped the preprocessing, and are only doing ROI analysis)
592. bet2 "${outdir}/dti_FA.nii.gz" "${outdir}/dti_FA_brain" -m
593. flirt -in "${outdir}/dti_FA_brain_mask.nii.gz" -ref "${outdir}/${smri}.nii.gz" -interp nearestneighbour -out "${outdir}/dti_FA_brain_mask_2_struct.nii.gz" -init "${outdir}/dti2struct.mat" -applyxfm
594. fslmaths "${outdir}/${smri}.nii.gz" -mul "${outdir}/dti_FA_brain_mask_2_struct.nii.gz" "${outdir}/${smri}_brain.nii.gz"
595. fi
597. flirt -ref "${template}" -in "${outdir}/${smri}_brain.nii.gz" -omat "${outdir}/struct2template_aff.mat"
598. fnirt --in="${outdir}/${smri}.nii.gz" --aff="${outdir}/struct2template_aff.mat" --cout="${outdir}/struct2template_warps" \
599. --ref="${template}" ${template_mask}--imprefm=1 \
600. --impinm=1 --imprefval=0 --impinval=0 --subsamp=4,4,2,2,1,1 --miter=5,5,5,5,5,10 --infwhm=8,6,5,4.5,3,2 --reffwhm=8,6,5,4,2,0 \
601. --lambda=300,150,100,50,40,30 --estint=1,1,1,1,1,0 --applyrefmask=1,1,1,1,1,1 --applyinmask=1 --warpres=10,10,10 --ssqlambda=1 \
602. --regmod=bending_energy --intmod=global_non_linear_with_bias --intorder=5 --biasres=50,50,50 --biaslambda=10000 --refderiv=0
603. applywarp --in="${outdir}/dti_FA.nii.gz" --ref="${template}" --warp="${outdir}/struct2template_warps" --premat="${outdir}/dti2struct.mat" --out="${outdir}/dti_FA_to_${template_abbreviation}.nii.gz"
604. applywarp --in="${outdir}/dti_MD.nii.gz" --ref="${template}" --warp="${outdir}/struct2template_warps" --premat="${outdir}/dti2struct.mat" --out="${outdir}/dti_MD_to_${template_abbreviation}.nii.gz"
605. if [ "$freg" == "1" ]; then echo "Transformation of the tensor to the template with applywarp";
606. applywarp --in="${outdir}/dti_tensor.nii.gz" --ref="${template}" --warp="${outdir}/struct2template_warps" --premat="${outdir}/dti2struct.mat" --out="${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz"
607. #applywarp --in="${outdir}/dxx.nii.gz" --ref="${template}" --warp="${outdir}/struct2template_warps" --premat="${outdir}/dti2struct.mat" --out="${outdir}/dxx_in_${template_abbreviation}.nii.gz"
608. #applywarp --in="${outdir}/dyy.nii.gz" --ref="${template}" --warp="${outdir}/struct2template_warps" --premat="${outdir}/dti2struct.mat" --out="${outdir}/dyy_in_${template_abbreviation}.nii.gz"
609. #applywarp --in="${outdir}/dzz.nii.gz" --ref="${template}" --warp="${outdir}/struct2template_warps" --premat="${outdir}/dti2struct.mat" --out="${outdir}/dzz_in_${template_abbreviation}.nii.gz"
610. elif [ "$freg" == "2" ]; then echo "Transformation of the tensor to the template with vecreg";
611. vecreg -i "${outdir}/dti_tensor.nii.gz" -r "${template}" -o "${outdir}/dti_tensor_in_struct.nii.gz" -t "${outdir}/dti2struct.mat"
612. vecreg -i "${outdir}/dti_tensor_in_struct.nii.gz" -r "${template}" -o "${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz" -w "${outdir}/struct2template_warps"
613. fi
614. else
615. if [ "$warp" == "0" ]; then
616. if [ ! -f "${outdir}/dti_FA_to_${template_abbreviation}.nii.gz" ]; then
617. echo "Linear registration to template with flirt and default options";
618. flirt -in "${outdir}/dti_FA.nii.gz" -ref "${template}" -out "${outdir}/dti_FA_to_${template_abbreviation}.nii.gz" -omat "${outdir}/FA_to_${template_abbreviation}.mat" -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12;
619. flirt -in "${outdir}/dti_MD.nii.gz" -ref "${template}" -out "${outdir}/dti_MD_to_${template_abbreviation}.nii.gz" -init "${outdir}/FA_to_${template_abbreviation}.mat" -applyxfm;
620. else echo "dti_FA registered to template exists and will NOT be overwritten: ${outdir}/dti_FA_to_${template_abbreviation}.nii.gz"; fi
621. if [ ! -f "${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz" ]; then
622. if [ "$freg" == "1" ]; then echo "Transformation of the tensor to the template with flirt";
623. flirt -in "${outdir}/dti_tensor.nii.gz" -ref "${template}" -out "${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz" -init "${outdir}/FA_to_${template_abbreviation}.mat" -applyxfm
624. #flirt -in "${outdir}/dxx.nii.gz" -ref "${template}" -out "${outdir}/dxx_in_${template_abbreviation}.nii.gz" -init "${outdir}/FA_to_${template_abbreviation}.mat" -applyxfm
625. #flirt -in "${outdir}/dyy.nii.gz" -ref "${template}" -out "${outdir}/dyy_in_${template_abbreviation}.nii.gz" -init "${outdir}/FA_to_${template_abbreviation}.mat" -applyxfm
626. #flirt -in "${outdir}/dzz.nii.gz" -ref "${template}" -out "${outdir}/dzz_in_${template_abbreviation}.nii.gz" -init "${outdir}/FA_to_${template_abbreviation}.mat" -applyxfm
627. elif [ "$freg" == "2" ]; then echo "Transformation of the tensor to the template with vecreg";
628. vecreg -i "${outdir}/dti_tensor.nii.gz" -r "${template}" -o "${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz" -t "${outdir}/FA_to_${template_abbreviation}.mat"
629. #vecreg -i "${outdir}/dxx.nii.gz" -r "${template}" -o "${outdir}/dxx_in_${template_abbreviation}.nii.gz" -t "${outdir}/FA_to_${template_abbreviation}.mat"
630. #vecreg -i "${outdir}/dyy.nii.gz" -r "${template}" -o "${outdir}/dyy_in_${template_abbreviation}.nii.gz" -t "${outdir}/FA_to_${template_abbreviation}.mat"
631. #vecreg -i "${outdir}/dzz.nii.gz" -r "${template}" -o "${outdir}/dzz_in_${template_abbreviation}.nii.gz" -t "${outdir}/FA_to_${template_abbreviation}.mat"
632. fi
633. else echo "dti_tensor registered to template exists and will NOT be overwritten: ${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz"; fi
634. elif [ "$warp" == "1" ]; then
635. if [ ! -f "${outdir}/dti_FA_to_${template_abbreviation}.nii.gz" ]; then
636. echo "Non-Linear registration to template with fnirt and default options (cf. fsl/etc/flirtsch/FA_2_FMRIB58_1mm.cnf)";
637. fnirt --in="${outdir}/dti_FA.nii.gz" --ref="${template}" ${template_mask}--cout="${outdir}/FA_to_${template_abbreviation}_warps" --imprefm=1 --impinm=1 --imprefval=0 --impinval=0 --subsamp=8,4,2,2 \
638. --miter=5,5,5,5 --infwhm=12,6,2,2 --reffwhm=12,6,2,2 --lambda=300,75,30,30 --estint=1,1,1,0 --warpres=10,10,10 --ssqlambda=1 \
639. --regmod=bending_energy --intmod=global_linear --refderiv=0
640. applywarp --in="${outdir}/dti_FA.nii.gz" --ref="${template}" --warp="${outdir}/FA_to_${template_abbreviation}_warps" --out="${outdir}/dti_FA_to_${template_abbreviation}.nii.gz"
641. applywarp --in="${outdir}/dti_MD.nii.gz" --ref="${template}" --warp="${outdir}/FA_to_${template_abbreviation}_warps" --out="${outdir}/dti_MD_to_${template_abbreviation}.nii.gz"
642. else echo "dti_FA registered to template exists and will NOT be overwritten: ${outdir}/dti_FA_to_${template_abbreviation}.nii.gz"; fi
643. if [ ! -f "${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz" ]; then
644. if [ "$freg" == "1" ]; then echo "Transformation of the tensor to the template with applywarp";
645. applywarp --in="${outdir}/dti_tensor.nii.gz" --ref="${template}" --warp="${outdir}/FA_to_${template_abbreviation}_warps" --out="${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz"
646. #applywarp --in="${outdir}/dxx.nii.gz" --ref="${template}" --warp="${outdir}/FA_to_${template_abbreviation}_warps" --out="${outdir}/dxx_in_${template_abbreviation}.nii.gz"
647. #applywarp --in="${outdir}/dyy.nii.gz" --ref="${template}" --warp="${outdir}/FA_to_${template_abbreviation}_warps" --out="${outdir}/dyy_in_${template_abbreviation}.nii.gz"
648. #applywarp --in="${outdir}/dzz.nii.gz" --ref="${template}" --warp="${outdir}/FA_to_${template_abbreviation}_warps" --out="${outdir}/dzz_in_${template_abbreviation}.nii.gz"
649. elif [ "$freg" == "2" ]; then echo "Transformation of the tensor to the template with vecreg";
650. vecreg -i "${outdir}/dti_tensor.nii.gz" -r "${template}" -o "${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz" -w "${outdir}/FA_to_${template_abbreviation}_warps"
651. fi
652. else echo "dti_tensor registered to template exists and will NOT be overwritten: ${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz"; fi
653. elif [ "$warp" == "2" ]; then
654. if [ ! -f "${outdir}/dti_FA_to_${template_abbreviation}.nii.gz" ]; then
655. echo "Linear (flirt) + Non-Linear (fnirt) registration to template";
656. flirt -in "${outdir}/dti_FA.nii.gz" -ref "${template}" -omat "${outdir}/FA_to_${template_abbreviation}_aff.mat" -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12
657. fnirt --in="${outdir}/dti_FA.nii.gz" --ref="${template}" ${template_mask}--aff="${outdir}/FA_to_${template_abbreviation}_aff.mat" \
658. --cout="${outdir}/FA_to_${template_abbreviation}_warps" --imprefm=1 --impinm=1 --imprefval=0 --impinval=0 --subsamp=8,4,2,2 \
659. --miter=5,5,5,5 --infwhm=12,6,2,2 --reffwhm=12,6,2,2 --lambda=300,75,30,30 --estint=1,1,1,0 --warpres=10,10,10 --ssqlambda=1 \
660. --regmod=bending_energy --intmod=global_linear --refderiv=0
661. applywarp --in="${outdir}/dti_FA.nii.gz" --ref="${template}" --warp="${outdir}/FA_to_${template_abbreviation}_warps" --out="${outdir}/dti_FA_to_${template_abbreviation}.nii.gz"
662. applywarp --in="${outdir}/dti_MD.nii.gz" --ref="${template}" --warp="${outdir}/FA_to_${template_abbreviation}_warps" --out="${outdir}/dti_MD_to_${template_abbreviation}.nii.gz"
663. else echo "dti_FA registered to template exists and will NOT be overwritten: ${outdir}/dti_FA_to_${template_abbreviation}.nii.gz"; fi
664. if [ ! -f "${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz" ]; then
665. if [ "$freg" == "1" ]; then echo "Transformation of the tensor to the template with applywarp";
666. applywarp --in="${outdir}/dti_tensor.nii.gz" --ref="${template}" --warp="${outdir}/FA_to_${template_abbreviation}_warps" --out="${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz"
667. #applywarp --in="${outdir}/dxx.nii.gz" --ref="${template}" --warp="${outdir}/FA_to_${template_abbreviation}_warps" --out="${outdir}/dxx_in_${template_abbreviation}.nii.gz"
668. #applywarp --in="${outdir}/dyy.nii.gz" --ref="${template}" --warp="${outdir}/FA_to_${template_abbreviation}_warps" --out="${outdir}/dyy_in_${template_abbreviation}.nii.gz"
669. #applywarp --in="${outdir}/dzz.nii.gz" --ref="${template}" --warp="${outdir}/FA_to_${template_abbreviation}_warps" --out="${outdir}/dzz_in_${template_abbreviation}.nii.gz"
670. elif [ "$freg" == "2" ]; then echo "Transformation of the tensor to the template with vecreg";
671. vecreg -i "${outdir}/dti_tensor.nii.gz" -r "${template}" -o "${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz" -w "${outdir}/FA_to_${template_abbreviation}_warps"
672. fi
673. else echo "dti_tensor registered to template exists and will NOT be overwritten: ${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz"; fi
674. fi
675. fi
676. fslroi "${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz" "${outdir}/dxx_in_${template_abbreviation}.nii.gz" 0 1
677. fslroi "${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz" "${outdir}/dyy_in_${template_abbreviation}.nii.gz" 3 1
678. fslroi "${outdir}/dti_tensor_in_${template_abbreviation}.nii.gz" "${outdir}/dzz_in_${template_abbreviation}.nii.gz" 5 1
679. dxx="${outdir}/dxx_in_${template_abbreviation}.nii.gz"
680. dyy="${outdir}/dyy_in_${template_abbreviation}.nii.gz"
681. dzz="${outdir}/dzz_in_${template_abbreviation}.nii.gz"
682. fa="${outdir}/dti_FA_to_${template_abbreviation}.nii.gz"
683. md="${outdir}/dti_MD_to_${template_abbreviation}.nii.gz"
684. elif [ "$template" == "0" ]; then #analysis in native space
685. echo "ALPS analysis in native space"
686. fslroi "${outdir}/dti_tensor.nii.gz" "${outdir}/dxx.nii.gz" 0 1
687. fslroi "${outdir}/dti_tensor.nii.gz" "${outdir}/dyy.nii.gz" 3 1
688. fslroi "${outdir}/dti_tensor.nii.gz" "${outdir}/dzz.nii.gz" 5 1
689. dxx="${outdir}/dxx.nii.gz"
690. dyy="${outdir}/dyy.nii.gz"
691. dzz="${outdir}/dzz.nii.gz"
692. fa="${outdir}/dti_FA.nii.gz"
693. md="${outdir}/dti_MD.nii.gz"
694. #if [ "$rois" == "${script_folder}/ROIs_JHU_ALPS/L_SCR.nii.gz,${script_folder}/ROIs_JHU_ALPS/R_SCR.nii.gz,${script_folder}/ROIs_JHU_ALPS/L_SLF.nii.gz,${script_folder}/ROIs_JHU_ALPS/R_SLF.nii.gz" ]; then
695. template=${FSLDIR}/data/atlases/JHU/JHU-ICBM-FA-1mm.nii.gz
696. template_abbreviation=JHU-FA
697. flirt -ref "${outdir}/dti_FA.nii.gz" -in "${template}" -out "${outdir}/dti_FA_${template_abbreviation}_to_native.nii.gz" -omat "${outdir}/${template_abbreviation}_to_native.mat" -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12
698. for r in $(echo $rois | tr -s ',' ' '); do
699. flirt -in "${r}" -ref "${outdir}/dti_FA.nii.gz" -out "${outdir}/"$(basename "$(basename "$(basename "$r" .gz)" .nii)" _in_${template_abbreviation})"_native.nii.gz" -init "${outdir}/${template_abbreviation}_to_native.mat" -applyxfm -interp nearestneighbour
700. done
701. proj_L=${outdir}/"$(basename "$(basename "$(basename "$(echo "${rois}" | cut -d ',' -f1)" .gz)" .nii)" _in_${template_abbreviation})"_native.nii.gz
702. proj_R=${outdir}/"$(basename "$(basename "$(basename "$(echo "${rois}" | cut -d ',' -f2)" .gz)" .nii)" _in_${template_abbreviation})"_native.nii.gz
703. assoc_L=${outdir}/"$(basename "$(basename "$(basename "$(echo "${rois}" | cut -d ',' -f3)" .gz)" .nii)" _in_${template_abbreviation})"_native.nii.gz
704. assoc_R=${outdir}/"$(basename "$(basename "$(basename "$(echo "${rois}" | cut -d ',' -f4)" .gz)" .nii)" _in_${template_abbreviation})"_native.nii.gz
705. fslmaths "${proj_L}" -add "${proj_R}" -add "${assoc_L}" -add "${assoc_R}" -bin "${outdir}/all_ROIs_native.nii.gz"
706. cluster -t 1 -i "${outdir}/all_ROIs_native.nii.gz" -o "${outdir}/all_ROIs_native.nii.gz"
707. #fi
708. fi
711. #GATHER STATS
712. mkdir -p "${outdir}/alps.stat"
713. echo "id,scanner,x_proj_L,x_assoc_L,y_proj_L,z_assoc_L,x_proj_R,x_assoc_R,y_proj_R,z_assoc_R,alps_L,alps_R,alps" > "${outdir}/alps.stat/alps.csv"
714. echo "id,scanner,diffusion_metric,proj_L,assoc_L,proj_R,assoc_R,mean_proj,mean_assoc" > "${outdir}/alps.stat/fa+md_alps.csv"
716. if [[ "$dwi1" == *".nii" ]]; then
717. id="$(basename "$dwi1" .nii)"
718. elif [[ $dwi1 == *".nii.gz" ]]; then
719. id="$(basename "$dwi1" .nii.gz)"
720. else
721. id="$(basename "$dwi1")"
722. fi
724. x_proj_L="$(fslstats "${dxx}" -k "${proj_L}" -m)"
725. x_assoc_L="$(fslstats "${dxx}" -k "${assoc_L}" -m)"
726. y_proj_L="$(fslstats "${dyy}" -k "${proj_L}" -m)"
727. z_assoc_L="$(fslstats "${dzz}" -k "${assoc_L}" -m)"
728. x_proj_R="$(fslstats "${dxx}" -k "${proj_R}" -m)"
729. x_assoc_R="$(fslstats "${dxx}" -k "${assoc_R}" -m)"
730. y_proj_R="$(fslstats "${dyy}" -k "${proj_R}" -m)"
731. z_assoc_R="$(fslstats "${dzz}" -k "${assoc_R}" -m)"
732. alps_L=`echo "(($x_proj_L+$x_assoc_L)/2)/(($y_proj_L+$z_assoc_L)/2)" | bc -l` #proj1 and assoc1 are left side, bc -l needed for decimal printing results
733. alps_R=`echo "(($x_proj_R+$x_assoc_R)/2)/(($y_proj_R+$z_assoc_R)/2)" | bc -l` #proj2 and assoc2 are right side, bc -l needed for decimal printing results
734. alps=`echo "($alps_R+$alps_L)/2" | bc -l`
736. echo "${id},${scanner1},${x_proj_L},${x_assoc_L},${y_proj_L},${z_assoc_L},${x_proj_R},${x_assoc_R},${y_proj_R},${z_assoc_R},${alps_L},${alps_R},${alps}" >> "${outdir}/alps.stat/alps.csv"
738. #FA and MD values from projection and association areas
739. for diff in "${fa}" "${md}"; do
740. pl="$(fslstats "${diff}" -k "${proj_L}" -m)"
741. pr="$(fslstats "${diff}" -k "${proj_R}" -m)"
742. al="$(fslstats "${diff}" -k "${assoc_L}" -m)"
743. ar="$(fslstats "${diff}" -k "${assoc_R}" -m)"
744. pmean=`echo "($pl+$pr)/2" | bc -l`
745. amean=`echo "($al+$ar)/2" | bc -l`
746. if [ "${diff}" == "${fa}" ]; then d="FA"; else d="MD"; fi
747. echo "${id},${scanner1},${d},${pl},${al},${pr},${ar},${pmean},${amean}" >> "${outdir}/alps.stat/fa+md_alps.csv"
748. done
749. elif [ "$rois" == "0" ]; then
750. echo "ROI analysis skipped by the user.";
751. fi
753. echo "Finito! Please cite this repository (https://github.com/gbarisano/alps/) and the paper:
754. Liu, X, Barisano, G, et al., Cross-Vendor Test-Retest Validation of Diffusion Tensor Image Analysis along the Perivascular Space (DTI-ALPS) for Evaluating Glymphatic System Function, Aging and Disease (2023)"

alps.sh at commit e6f58e7, under MIT · at the source