OSCR

Regulation of autism-related self-injurious behavior by electrical stimulation of corticostriatal circuits in mice and humans.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

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  1. [1] § MATERIALS AND METHODS › Statistical analyses › Deformation-based morphometry ↔ dbm.sh, lines 394–449 · score 0.62 · deformation field, Jacobian determinants, geometric, mask, DBM
  2. [2] § MATERIALS AND METHODS › Statistical analyses › Deformation-based morphometry ↔ twolevel_dbm.py, lines 742–810 · score 0.53 · Jacobian determinants, mni, deformation, morphometry, DBM, field

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Shell · 592 lines · 26 KB · other · 1 match

  1. #!/usr/bin/env bash
  2. # ARG_HELP([DBM post-processing for modelbuild.sh from optimized_antsMultivariateTemplateConstruction])
  3. # ARG_OPTIONAL_SINGLE([output-dir],[],[Output directory for modelbuild],[output])
  4. # ARG_OPTIONAL_BOOLEAN([float],[],[Use float instead of double for calculations (reduce memory requirements, reduce precision)],[])
  5. # ARG_OPTIONAL_SINGLE([mask],[],[Mask file for average to improve delin estimates],[])
  6. # ARG_OPTIONAL_SINGLE([target-space],[],[Target space for DBM outputs, requires --final-target be used with modelbuild.sh],[unbiased])
  7. # ARG_TYPE_GROUP_SET([spacegroup],[SPACE],[target-space],[unbiased,final-target])
  8. # ARG_OPTIONAL_SINGLE([delin-affine-ratio],[],[Ratio of voxels within mask used to estimate delin affine],[0.25])
  9. # ARG_OPTIONAL_BOOLEAN([use-geometric],[],[Use geometric estimate of Jacobian instead of finite-difference],[on])
  10. # ARG_OPTIONAL_SINGLE([jacobian-smooth],[],[Comma separated list of smoothing gaussian FWHM, append "vox" for voxels, "mm" for millimeters],[4vox])
  11. # ARG_OPTIONAL_SINGLE([walltime],[],[Walltime for short running stages (averaging, resampling)],[00:15:00])
  12. # ARG_OPTIONAL_BOOLEAN([block],[],[For qbatch SGE, PBS and SLURM, blocks execution until jobs are finished.],[])
  13. # ARG_OPTIONAL_BOOLEAN([debug],[],[Debug mode, print all commands to stdout],[])
  14. # ARG_OPTIONAL_BOOLEAN([dry-run],[],[Dry run, don't run any commands, implies debug],[])
  15. # ARG_OPTIONAL_SINGLE([jobname-prefix],[],[Prefix to add to front of job names, used by twolevel wrapper],[])
  16. # ARG_POSITIONAL_INF([inputs],[Input text files, one line per input, one file per spectra],[1])
  17. # ARGBASH_SET_INDENT([ ])
  18. # ARGBASH_GO()
  19. # needed because of Argbash --> m4_ignore([
  20. ### START OF CODE GENERATED BY Argbash v2.10.0 one line above ###
  21. # Argbash is a bash code generator used to get arguments parsing right.
  22. # Argbash is FREE SOFTWARE, see https://argbash.dev for more info
  25. die()
  26. {
  27. local _ret="${2:-1}"
  28. test "${_PRINT_HELP:-no}" = yes && print_help >&2
  29. echo "$1" >&2
  30. exit "${_ret}"
  31. }
  33. # validators
  35. spacegroup()
  36. {
  37. local _allowed=("unbiased" "final-target") _seeking="$1"
  38. for element in "${_allowed[@]}"
  39. do
  40. test "$element" = "$_seeking" && echo "$element" && return 0
  41. done
  42. die "Value '$_seeking' (of argument '$2') doesn't match the list of allowed values: 'unbiased' and 'final-target'" 4
  43. }
  46. begins_with_short_option()
  47. {
  48. local first_option all_short_options='h'
  49. first_option="${1:0:1}"
  50. test "$all_short_options" = "${all_short_options/$first_option/}" && return 1 || return 0
  51. }
  53. # THE DEFAULTS INITIALIZATION - POSITIONALS
  54. _positionals=()
  55. _arg_inputs=('' )
  56. # THE DEFAULTS INITIALIZATION - OPTIONALS
  57. _arg_output_dir="output"
  58. _arg_float="off"
  59. _arg_mask=
  60. _arg_target_space="unbiased"
  61. _arg_delin_affine_ratio="0.25"
  62. _arg_use_geometric="on"
  63. _arg_jacobian_smooth="4vox"
  64. _arg_walltime="00:15:00"
  65. _arg_block="off"
  66. _arg_debug="off"
  67. _arg_dry_run="off"
  68. _arg_jobname_prefix=
  71. print_help()
  72. {
  73. printf '%s\n' "DBM post-processing for modelbuild.sh from optimized_antsMultivariateTemplateConstruction"
  74. printf 'Usage: %s [-h|--help] [--output-dir <arg>] [--(no-)float] [--mask <arg>] [--target-space <SPACE>] [--delin-affine-ratio <arg>] [--(no-)use-geometric] [--jacobian-smooth <arg>] [--walltime <arg>] [--(no-)block] [--(no-)debug] [--(no-)dry-run] [--jobname-prefix <arg>] <inputs-1> [<inputs-2>] ... [<inputs-n>] ...\n' "$0"
  75. printf '\t%s\n' "<inputs>: Input text files, one line per input, one file per spectra"
  76. printf '\t%s\n' "-h, --help: Prints help"
  77. printf '\t%s\n' "--output-dir: Output directory for modelbuild (default: 'output')"
  78. printf '\t%s\n' "--float, --no-float: Use float instead of double for calculations (reduce memory requirements, reduce precision) (off by default)"
  79. printf '\t%s\n' "--mask: Mask file for average to improve delin estimates (no default)"
  80. printf '\t%s\n' "--target-space: Target space for DBM outputs, requires --final-target be used with modelbuild.sh. Can be one of: 'unbiased' and 'final-target' (default: 'unbiased')"
  81. printf '\t%s\n' "--delin-affine-ratio: Ratio of voxels within mask used to estimate delin affine (default: '0.25')"
  82. printf '\t%s\n' "--use-geometric, --no-use-geometric: Use geometric estimate of Jacobian instead of finite-difference (on by default)"
  83. printf '\t%s\n' "--jacobian-smooth: Comma separated list of smoothing gaussian FWHM, append \"vox\" for voxels, \"mm\" for millimeters (default: '4vox')"
  84. printf '\t%s\n' "--walltime: Walltime for short running stages (averaging, resampling) (default: '00:15:00')"
  85. printf '\t%s\n' "--block, --no-block: For qbatch SGE, PBS and SLURM, blocks execution until jobs are finished. (off by default)"
  86. printf '\t%s\n' "--debug, --no-debug: Debug mode, print all commands to stdout (off by default)"
  87. printf '\t%s\n' "--dry-run, --no-dry-run: Dry run, don't run any commands, implies debug (off by default)"
  88. printf '\t%s\n' "--jobname-prefix: Prefix to add to front of job names, used by twolevel wrapper (no default)"
  89. }
  92. parse_commandline()
  93. {
  94. _positionals_count=0
  95. while test $# -gt 0
  96. do
  97. _key="$1"
  98. case "$_key" in
  99. -h|--help)
  100. print_help
  101. exit 0
  102. ;;
  103. -h*)
  104. print_help
  105. exit 0
  106. ;;
  107. --output-dir)
  108. test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
  109. _arg_output_dir="$2"
  110. shift
  111. ;;
  112. --output-dir=*)
  113. _arg_output_dir="${_key##--output-dir=}"
  114. ;;
  115. --no-float|--float)
  116. _arg_float="on"
  117. test "${1:0:5}" = "--no-" && _arg_float="off"
  118. ;;
  119. --mask)
  120. test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
  121. _arg_mask="$2"
  122. shift
  123. ;;
  124. --mask=*)
  125. _arg_mask="${_key##--mask=}"
  126. ;;
  127. --target-space)
  128. test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
  129. _arg_target_space="$(spacegroup "$2" "target-space")" || exit 1
  130. shift
  131. ;;
  132. --target-space=*)
  133. _arg_target_space="$(spacegroup "${_key##--target-space=}" "target-space")" || exit 1
  134. ;;
  135. --delin-affine-ratio)
  136. test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
  137. _arg_delin_affine_ratio="$2"
  138. shift
  139. ;;
  140. --delin-affine-ratio=*)
  141. _arg_delin_affine_ratio="${_key##--delin-affine-ratio=}"
  142. ;;
  143. --no-use-geometric|--use-geometric)
  144. _arg_use_geometric="on"
  145. test "${1:0:5}" = "--no-" && _arg_use_geometric="off"
  146. ;;
  147. --jacobian-smooth)
  148. test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
  149. _arg_jacobian_smooth="$2"
  150. shift
  151. ;;
  152. --jacobian-smooth=*)
  153. _arg_jacobian_smooth="${_key##--jacobian-smooth=}"
  154. ;;
  155. --walltime)
  156. test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
  157. _arg_walltime="$2"
  158. shift
  159. ;;
  160. --walltime=*)
  161. _arg_walltime="${_key##--walltime=}"
  162. ;;
  163. --no-block|--block)
  164. _arg_block="on"
  165. test "${1:0:5}" = "--no-" && _arg_block="off"
  166. ;;
  167. --no-debug|--debug)
  168. _arg_debug="on"
  169. test "${1:0:5}" = "--no-" && _arg_debug="off"
  170. ;;
  171. --no-dry-run|--dry-run)
  172. _arg_dry_run="on"
  173. test "${1:0:5}" = "--no-" && _arg_dry_run="off"
  174. ;;
  175. --jobname-prefix)
  176. test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
  177. _arg_jobname_prefix="$2"
  178. shift
  179. ;;
  180. --jobname-prefix=*)
  181. _arg_jobname_prefix="${_key##--jobname-prefix=}"
  182. ;;
  183. *)
  184. _last_positional="$1"
  185. _positionals+=("$_last_positional")
  186. _positionals_count=$((_positionals_count + 1))
  187. ;;
  188. esac
  189. shift
  190. done
  191. }
  194. handle_passed_args_count()
  195. {
  196. local _required_args_string="'inputs'"
  197. test "${_positionals_count}" -ge 1 || _PRINT_HELP=yes die "FATAL ERROR: Not enough positional arguments - we require at least 1 (namely: $_required_args_string), but got only ${_positionals_count}." 1
  198. }
  201. assign_positional_args()
  202. {
  203. local _positional_name _shift_for=$1
  204. _positional_names="_arg_inputs "
  205. _our_args=$((${#_positionals[@]} - 1))
  206. for ((ii = 0; ii < _our_args; ii++))
  207. do
  208. _positional_names="$_positional_names _arg_inputs[$((ii + 1))]"
  209. done
  211. shift "$_shift_for"
  212. for _positional_name in ${_positional_names}
  213. do
  214. test $# -gt 0 || break
  215. eval "$_positional_name=\${1}" || die "Error during argument parsing, possibly an Argbash bug." 1
  216. shift
  217. done
  218. }
  220. parse_commandline "$@"
  221. handle_passed_args_count
  222. assign_positional_args 1 "${_positionals[@]}"
  224. # OTHER STUFF GENERATED BY Argbash
  225. # Validation of values
  228. ### END OF CODE GENERATED BY Argbash (sortof) ### ])
  229. # [ <-- needed because of Argbash
  231. set -uo pipefail
  232. set -eE -o functrace
  234. # Load up helper scripts and define helper variables
  235. # shellcheck source=helpers.sh
  236. source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/helpers.sh"
  238. # Set magic variables for current file, directory, os, etc.
  239. __file="${__dir}/$(basename "${BASH_SOURCE[${__b3bp_tmp_source_idx:-0}]}")"
  240. __base="$(basename "${__file}" .sh)"
  241. # shellcheck disable=SC2034,SC2015
  242. __invocation="$(printf %q "${__file}")$( (($#)) && printf ' %q' "$@" || true)"
  244. # Preflight check for required programs
  245. preflight_check
  247. # Setup a directory which contains all commands run
  248. # for this invocation
  249. mkdir -p ${_arg_output_dir}/dbm/jobs/${__datetime}
  250. mkdir -p ${_arg_output_dir}/dbm/logs/${__datetime}
  251. export QBATCH_SCRIPT_FOLDER="${_arg_output_dir}/dbm/qbatch/${__datetime}"
  253. # Store the full command line for each run
  254. echo ${__invocation} >${_arg_output_dir}/dbm/jobs/${__datetime}/invocation
  256. info "Checking input files"
  258. # Load input file into array
  259. if [[ ! -s ${_arg_inputs[0]} ]]; then
  260. failure "Input file ${_arg_inputs[0]} is non-existent or zero size"
  261. else
  262. mapfile -t _arg_inputs <${_arg_inputs[0]}
  263. fi
  265. for file in "${_arg_inputs[@]}"; do
  266. if [[ ! -s ${file} ]]; then
  267. failure "Input file ${file} is non-existent or zero size"
  268. fi
  269. done
  271. # Enable float mode for ants commands
  272. if [[ ${_arg_float} == "on" ]]; then
  273. _arg_float="--float"
  274. else
  275. _arg_float=""
  276. fi
  278. # Enable block for qbatch job submission
  279. if [[ ${_arg_block} == "on" ]]; then
  280. _arg_block="--block"
  281. else
  282. _arg_block=""
  283. fi
  285. # Convert smoothing jacobians to a list
  286. IFS=',' read -r -a _arg_jacobian_smooth <<<${_arg_jacobian_smooth}
  288. # Preflight check for required programs
  289. preflight_check
  291. # Make output directories
  292. mkdir -p ${_arg_output_dir}/dbm/intermediate/delin/{affine,warp,jacobian}
  293. mkdir -p ${_arg_output_dir}/dbm/intermediate/nlin/jacobian
  294. mkdir -p ${_arg_output_dir}/dbm/intermediate/affine/{warp,jacobian}
  295. mkdir -p ${_arg_output_dir}/dbm/jacobian/{final-target,}/{relative,full}//smooth
  297. # Convert geometric option to ANTs option
  298. if [[ ${_arg_use_geometric} == "on" ]]; then
  299. _arg_use_geometric=1
  300. else
  301. _arg_use_geometric=0
  302. fi
  304. _arg_log_jacobian=1
  306. # Generate jacobian from nlin field
  307. # Log, values > 0, voxel expands towards subject (i.e. subject voxel is larger)
  308. # Log, values < 0, voxel contracts towards subject (i.e. subject voxel is smaller)
  309. info "Computing Jacobians from non-linear warp fields"
  310. for file in "${_arg_inputs[@]}"; do
  311. if [[ ! -s ${_arg_output_dir}/final/transforms/$(basename ${file} | extension_strip)_1Warp.nii.gz ]]; then
  312. failure "Expected deformation file ${_arg_output_dir}/final/transforms/$(basename ${file} | extension_strip)_1Warp.nii.gz does not exist"
  313. fi
  314. if [[ ! -s ${_arg_output_dir}/dbm/intermediate/nlin/jacobian/$(basename ${file} | extension_strip).nii.gz ]]; then
  315. echo "CreateJacobianDeterminantImage 3 ${_arg_output_dir}/final/transforms/$(basename ${file} | extension_strip)_1Warp.nii.gz \
  316. ${_arg_output_dir}/dbm/intermediate/nlin/jacobian/$(basename ${file} | extension_strip).nii.gz ${_arg_log_jacobian} ${_arg_use_geometric}"
  317. fi
  318. done >${_arg_output_dir}/dbm/jobs/${__datetime}/nlin_jacobian
  320. debug "$(cat ${_arg_output_dir}/dbm/jobs/${__datetime}/nlin_jacobian)"
  321. if [[ ${_arg_dry_run} == "off" ]]; then
  322. qbatch ${_arg_block} --logdir ${_arg_output_dir}/dbm/logs/${__datetime} \
  323. --walltime ${_arg_walltime} \
  324. -N ${_arg_jobname_prefix}dbm_${__datetime}_nlin_jacobian \
  325. ${_arg_output_dir}/dbm/jobs/${__datetime}/nlin_jacobian
  326. fi
  328. # Generate warp field from affine transform
  329. info "Computing warp fields from affine transforms"
  330. for file in "${_arg_inputs[@]}"; do
  331. if [[ ! -s ${_arg_output_dir}/dbm/intermediate/affine/warp/$(basename ${file} | extension_strip).nii.gz ]]; then
  332. echo "antsApplyTransforms -d 3 --verbose ${_arg_float} \
  333. -r ${_arg_output_dir}/final/average/template_sharpen_shapeupdate.nii.gz \
  334. -t ${_arg_output_dir}/final/transforms/$(basename ${file} | extension_strip)_0GenericAffine.mat \
  335. -o [ ${_arg_output_dir}/dbm/intermediate/affine/warp/$(basename ${file} | extension_strip).nii.gz,1 ]"
  336. fi
  337. done >${_arg_output_dir}/dbm/jobs/${__datetime}/affine_warp
  339. debug "$(cat ${_arg_output_dir}/dbm/jobs/${__datetime}/affine_warp)"
  340. if [[ ${_arg_dry_run} == "off" ]]; then
  341. qbatch ${_arg_block} --logdir ${_arg_output_dir}/dbm/logs/${__datetime} \
  342. --walltime ${_arg_walltime} \
  343. -N ${_arg_jobname_prefix}dbm_${__datetime}_affine_warp \
  344. ${_arg_output_dir}/dbm/jobs/${__datetime}/affine_warp
  345. fi
  347. # Generate jacobian from affine warp field
  348. # Log, values > 0, voxel expands towards subject (i.e. subject voxel is larger)
  349. # Log, values < 0, voxel contracts towards subject (i.e. subject voxel is smaller)
  350. info "Computing Jacobians from affine warp fields"
  351. for file in "${_arg_inputs[@]}"; do
  352. if [[ ! -s ${_arg_output_dir}/dbm/intermediate/affine/jacobian/$(basename ${file} | extension_strip).nii.gz ]]; then
  353. echo "CreateJacobianDeterminantImage 3 ${_arg_output_dir}/dbm/intermediate/affine/warp/$(basename ${file} | extension_strip).nii.gz \
  354. ${_arg_output_dir}/dbm/intermediate/affine/jacobian/$(basename ${file} | extension_strip).nii.gz ${_arg_log_jacobian} ${_arg_use_geometric}"
  355. fi
  356. done >${_arg_output_dir}/dbm/jobs/${__datetime}/affine_jacobian
  358. debug "$(cat ${_arg_output_dir}/dbm/jobs/${__datetime}/affine_jacobian)"
  359. if [[ ${_arg_dry_run} == "off" ]]; then
  360. qbatch ${_arg_block} --logdir ${_arg_output_dir}/dbm/logs/${__datetime} \
  361. --walltime ${_arg_walltime} \
  362. -N ${_arg_jobname_prefix}dbm_${__datetime}_affine_jacobian \
  363. --depend ${_arg_jobname_prefix}dbm_${__datetime}_affine_warp \
  364. ${_arg_output_dir}/dbm/jobs/${__datetime}/affine_jacobian
  365. fi
  367. # Check for mask to use for delin
  368. if [[ -s ${_arg_mask} ]]; then
  369. info "Using supplied file ${_arg_mask} for delin calculation"
  370. elif [[ -s ${_arg_output_dir}/final/average/mask_shapeupdate.nii.gz ]]; then
  371. info "Using modelbuild mask ${_arg_output_dir}/final/average/mask_shapeupdate.nii.gz for delin calculation"
  372. _arg_mask=${_arg_output_dir}/final/average/mask_shapeupdate.nii.gz
  373. else
  374. if [[ ! -s ${_arg_output_dir}/dbm/intermediate/mask.nii.gz ]]; then
  375. info "No average mask available (provide via --mask), estimating mask using thresholding for delin calculation"
  376. # Otsu threshold, erode, get largest component, dilate
  377. echo "ThresholdImage 3 ${_arg_output_dir}/final/average/template_sharpen_shapeupdate.nii.gz \
  378. ${_arg_output_dir}/dbm/intermediate/mask.nii.gz Otsu 1 && \
  379. iMath 3 ${_arg_output_dir}/dbm/intermediate/mask.nii.gz ME ${_arg_output_dir}/dbm/intermediate/mask.nii.gz 1 1 ball 1 && \
  380. ImageMath 3 ${_arg_output_dir}/dbm/intermediate/mask.nii.gz GetLargestComponent ${_arg_output_dir}/dbm/intermediate/mask.nii.gz && \
  381. iMath 3 ${_arg_output_dir}/dbm/intermediate/mask.nii.gz MD ${_arg_output_dir}/dbm/intermediate/mask.nii.gz 1 1 ball 1"
  382. _arg_mask=${_arg_output_dir}/dbm/intermediate/mask.nii.gz
  383. fi
  384. fi >${_arg_output_dir}/dbm/jobs/${__datetime}/delin_mask
  386. debug "$(cat ${_arg_output_dir}/dbm/jobs/${__datetime}/delin_mask)"
  387. if [[ ${_arg_dry_run} == "off" && -s ${_arg_output_dir}/dbm/jobs/${__datetime}/delin_mask ]]; then
  388. qbatch ${_arg_block} --logdir ${_arg_output_dir}/dbm/logs/${__datetime} \
  389. --walltime ${_arg_walltime} \
  390. -N ${_arg_jobname_prefix}dbm_${__datetime}_delin_mask \
  391. -- bash ${_arg_output_dir}/dbm/jobs/${__datetime}/delin_mask
  392. fi
  394. # Generate delin affine from warp field
  395. info "Estimate delin affine from nlin warp fields"
  396. for file in "${_arg_inputs[@]}"; do
  397. if [[ ! -s ${_arg_output_dir}/dbm/intermediate/delin/affine/$(basename ${file} | extension_strip).mat ]]; then
  398. echo "ANTSUseDeformationFieldToGetAffineTransform ${_arg_output_dir}/final/transforms/$(basename ${file} | extension_strip)_1Warp.nii.gz \
  399. ${_arg_delin_affine_ratio} affine ${_arg_output_dir}/dbm/intermediate/delin/affine/$(basename ${file} | extension_strip).mat \
  400. ${_arg_mask}"
  401. fi
  402. done >${_arg_output_dir}/dbm/jobs/${__datetime}/delin_affine_from_warp
  404. debug "$(cat ${_arg_output_dir}/dbm/jobs/${__datetime}/delin_affine_from_warp)"
  405. if [[ ${_arg_dry_run} == "off" ]]; then
  406. qbatch ${_arg_block} --logdir ${_arg_output_dir}/dbm/logs/${__datetime} \
  407. --walltime ${_arg_walltime} \
  408. -N ${_arg_jobname_prefix}dbm_${__datetime}_delin_affine_from_warp \
  409. --depend ${_arg_jobname_prefix}dbm_${__datetime}_delin_mask \
  410. ${_arg_output_dir}/dbm/jobs/${__datetime}/delin_affine_from_warp
  411. fi
  413. # Generate warp from delin affine
  414. info "Generate composite warp field from delin affine"
  415. for file in "${_arg_inputs[@]}"; do
  416. if [[ ! -s ${_arg_output_dir}/dbm/intermediate/delin/warp/$(basename ${file} | extension_strip).nii.gz ]]; then
  417. echo "antsApplyTransforms -d 3 --verbose ${_arg_float} \
  418. -r ${_arg_output_dir}/final/average/template_sharpen_shapeupdate.nii.gz \
  419. -t [ ${_arg_output_dir}/dbm/intermediate/delin/affine/$(basename ${file} | extension_strip).mat,1 ] \
  420. -o [ ${_arg_output_dir}/dbm/intermediate/delin/warp/$(basename ${file} | extension_strip).nii.gz,1 ]"
  421. fi
  422. done >${_arg_output_dir}/dbm/jobs/${__datetime}/delin_warp_from_delin_affine
  424. debug "$(cat ${_arg_output_dir}/dbm/jobs/${__datetime}/delin_warp_from_delin_affine)"
  425. if [[ ${_arg_dry_run} == "off" ]]; then
  426. qbatch ${_arg_block} --logdir ${_arg_output_dir}/dbm/logs/${__datetime} \
  427. --walltime ${_arg_walltime} \
  428. -N ${_arg_jobname_prefix}dbm_${__datetime}_delin_warp_from_delin_affine \
  429. --depend ${_arg_jobname_prefix}dbm_${__datetime}_delin_affine_from_warp \
  430. ${_arg_output_dir}/dbm/jobs/${__datetime}/delin_warp_from_delin_affine
  431. fi
  433. # Generate jacobians from delin warp field
  434. info "Computing Jacobians from delin affine warp fields"
  435. for file in "${_arg_inputs[@]}"; do
  436. if [[ ! -s ${_arg_output_dir}/dbm/intermediate/delin/jacobian/$(basename ${file} | extension_strip).nii.gz ]]; then
  437. echo "CreateJacobianDeterminantImage 3 ${_arg_output_dir}/dbm/intermediate/delin/warp/$(basename ${file} | extension_strip).nii.gz \
  438. ${_arg_output_dir}/dbm/intermediate/delin/jacobian/$(basename ${file} | extension_strip).nii.gz ${_arg_log_jacobian} ${_arg_use_geometric}"
  439. fi
  440. done >${_arg_output_dir}/dbm/jobs/${__datetime}/jacobian_from_delin_warp
  442. debug "$(cat ${_arg_output_dir}/dbm/jobs/${__datetime}/jacobian_from_delin_warp)"
  443. if [[ ${_arg_dry_run} == "off" ]]; then
  444. qbatch ${_arg_block} --logdir ${_arg_output_dir}/dbm/logs/${__datetime} \
  445. --walltime ${_arg_walltime} \
  446. -N ${_arg_jobname_prefix}dbm_${__datetime}_jacobian_from_delin_warp \
  447. --depend ${_arg_jobname_prefix}dbm_${__datetime}_delin_warp_from_delin_affine \
  448. ${_arg_output_dir}/dbm/jobs/${__datetime}/jacobian_from_delin_warp
  449. fi
  451. # Generate final full jacobians
  452. info "Generating Full Jacobians"
  453. for file in "${_arg_inputs[@]}"; do
  454. if [[ ! -s ${_arg_output_dir}/dbm/jacobian/full/$(basename ${file} | extension_strip).nii.gz ]]; then
  455. echo "ImageMath 3 \
  456. ${_arg_output_dir}/dbm/jacobian/full/$(basename ${file} | extension_strip).nii.gz \
  457. + ${_arg_output_dir}/dbm/intermediate/affine/jacobian/$(basename ${file} | extension_strip).nii.gz \
  458. ${_arg_output_dir}/dbm/intermediate/nlin/jacobian/$(basename ${file} | extension_strip).nii.gz"
  459. fi
  460. done >${_arg_output_dir}/dbm/jobs/${__datetime}/gen_full_jacobian
  462. debug "$(cat ${_arg_output_dir}/dbm/jobs/${__datetime}/gen_full_jacobian)"
  463. if [[ ${_arg_dry_run} == "off" ]]; then
  464. qbatch ${_arg_block} --logdir ${_arg_output_dir}/dbm/logs/${__datetime} \
  465. --walltime ${_arg_walltime} \
  466. -N ${_arg_jobname_prefix}dbm_${__datetime}_gen_full_jacobian \
  467. --depend ${_arg_jobname_prefix}dbm_${__datetime}_affine_jacobian \
  468. --depend ${_arg_jobname_prefix}dbm_${__datetime}_nlin_jacobian \
  469. ${_arg_output_dir}/dbm/jobs/${__datetime}/gen_full_jacobian
  470. fi
  472. # Generate final relative jacobians
  473. info "Generating Relative Jacobians"
  474. for file in "${_arg_inputs[@]}"; do
  475. if [[ ! -s ${_arg_output_dir}/dbm/jacobian/relative/$(basename ${file} | extension_strip).nii.gz ]]; then
  476. echo "ImageMath 3 \
  477. ${_arg_output_dir}/dbm/jacobian/relative/$(basename ${file} | extension_strip).nii.gz \
  478. + ${_arg_output_dir}/dbm/intermediate/delin/jacobian/$(basename ${file} | extension_strip).nii.gz \
  479. ${_arg_output_dir}/dbm/intermediate/nlin/jacobian/$(basename ${file} | extension_strip).nii.gz"
  480. fi
  481. done >${_arg_output_dir}/dbm/jobs/${__datetime}/gen_rel_jacobian
  483. debug "$(cat ${_arg_output_dir}/dbm/jobs/${__datetime}/gen_rel_jacobian)"
  484. if [[ ${_arg_dry_run} == "off" ]]; then
  485. qbatch ${_arg_block} --logdir ${_arg_output_dir}/dbm/logs/${__datetime} \
  486. --walltime ${_arg_walltime} \
  487. -N ${_arg_jobname_prefix}dbm_${__datetime}_gen_rel_jacobian \
  488. --depend ${_arg_jobname_prefix}dbm_${__datetime}_nlin_jacobian \
  489. --depend ${_arg_jobname_prefix}dbm_${__datetime}_jacobian_from_delin_warp \
  490. ${_arg_output_dir}/dbm/jobs/${__datetime}/gen_rel_jacobian
  491. fi
  493. # # Generate unlogged relative jacobians
  494. # if [[ ${_arg_unlog_jacobian} == "on" ]]; then
  495. # info "Generating Un-logged Relative Jacobians"
  496. # for file in "${_arg_inputs[@]}"; do
  497. # if [[ ! -s ${_arg_output_dir}/dbm/jacobian/relative/unlog/$(basename ${file} | extension_strip).nii.gz ]]; then
  498. # command=("python" "-c" "'import SimpleITK as sitk; sitk.WriteImage(sitk.Exp(sitk.ReadImage(\"${_arg_output_dir}/dbm/jacobian/relative/$(basename ${file} | extension_strip).nii.gz\")),\"${_arg_output_dir}/dbm/jacobian/relative/unlog/$(basename ${file} | extension_strip).nii.gz\")'" )
  499. # echo "${command[@]}"
  500. # fi
  501. # done >${_arg_output_dir}/dbm/jobs/${__datetime}/gen_unlog_rel_jacobian
  503. # debug "$(cat ${_arg_output_dir}/dbm/jobs/${__datetime}/gen_unlog_rel_jacobian)"
  504. # if [[ ${_arg_dry_run} == "off" ]]; then
  505. # qbatch ${_arg_block} --logdir ${_arg_output_dir}/logs/${__datetime} \
  506. # --walltime ${_arg_walltime} \
  507. # -N ${_arg_jobname_prefix}dbm_${__datetime}_gen_unlog_rel_jacobian \
  508. # --depend ${_arg_jobname_prefix}dbm_${__datetime}_gen_frel_jacobian \
  509. # ${_arg_output_dir}/dbm/jobs/${__datetime}/gen_unlog_rel_jacobian
  510. # fi
  511. # fi
  513. # If requested, resample DBM outputs into final-target space
  514. if [[ ${_arg_target_space} == "final-target" ]]; then
  515. mkdir -p ${_arg_output_dir}/dbm/jacobian/{relative,full}/{unlog,}/final-target
  516. info "Resampling DBM"
  517. for file in "${_arg_inputs[@]}"; do
  518. for type in relative full; do
  519. if [[ ! -s ${_arg_output_dir}/dbm/jacobian/final-target/${type}/$(basename ${file} | extension_strip).nii.gz ]]; then
  520. echo antsApplyTransforms -d 3 --verbose -n Linear \
  521. -i ${_arg_output_dir}/dbm/jacobian/${type}/$(basename ${file} | extension_strip).nii.gz \
  522. -o ${_arg_output_dir}/dbm/jacobian/final-target/${type}/$(basename ${file} | extension_strip).nii.gz \
  523. -t ${_arg_output_dir}/final-target/to_target_1Warp.nii.gz \
  524. -t ${_arg_output_dir}/final-target/to_target_0GenericAffine.mat \
  525. -r ${_arg_output_dir}/final-target/final_target.nii.gz
  526. fi
  527. done
  528. # if [[ ${_arg_unlog_jacobian} == "on" ]]; then
  529. # if [[ ! -s ${_arg_output_dir}/dbm/jacobian/relative/unlog/final-target/$(basename ${file} | extension_strip).nii.gz ]]; then
  530. # true
  531. # fi
  532. # if [[ ! -s ${_arg_output_dir}/dbm/jacobian/full/unlog/final-target/$(basename ${file} | extension_strip).nii.gz ]]; then
  533. # true
  534. # fi
  535. # fi
  536. done >${_arg_output_dir}/dbm/jobs/${__datetime}/resample_jacobians_final_target
  538. debug "$(cat ${_arg_output_dir}/dbm/jobs/${__datetime}/resample_jacobians_final_target)"
  539. if [[ ${_arg_dry_run} == "off" ]]; then
  540. qbatch ${_arg_block} --logdir ${_arg_output_dir}/dbm/logs/${__datetime} \
  541. --walltime ${_arg_walltime} \
  542. -N ${_arg_jobname_prefix}dbm_${__datetime}_resample_jacobians_final_target \
  543. --depend ${_arg_jobname_prefix}dbm_${__datetime}_gen_rel_jacobian \
  544. --depend ${_arg_jobname_prefix}dbm_${__datetime}_gen_full_jacobian \
  545. ${_arg_output_dir}/dbm/jobs/${__datetime}/resample_jacobians_final_target
  546. fi
  547. fi
  549. # Smooth jacobians files
  550. info "Smoothing Jacobians"
  551. for file in "${_arg_inputs[@]}"; do
  552. for fwhm in "${_arg_jacobian_smooth[@]}"; do
  553. sigma_num=$(calc "$(echo ${fwhm} | grep -o -E '^[0-9]+')/(2*sqrt(2*log(2)))")
  554. if [[ ${fwhm} =~ [0-9]+mm$ ]]; then
  555. fwhm_type=1
  556. elif [[ ${fwhm} =~ [0-9]+vox$ ]]; then
  557. fwhm_type=0
  558. else
  559. failure "Parse error for FWHM entry \"${fwhm}\", must end with vox or mm"
  560. fi
  561. for type in relative full; do
  562. if [[ ! -s ${_arg_output_dir}/dbm/jacobian/${type}/smooth/$(basename ${file} | extension_strip)_fwhm_${fwhm}.nii.gz ]]; then
  563. echo SmoothImage 3 \
  564. ${_arg_output_dir}/dbm/jacobian/${type}/$(basename ${file} | extension_strip).nii.gz \
  565. ${sigma_num} \
  566. ${_arg_output_dir}/dbm/jacobian/${type}/smooth/$(basename ${file} | extension_strip)_fwhm_${fwhm}.nii.gz ${fwhm_type} 0
  567. fi
  568. if [[ ${_arg_target_space} == "final-target" ]]; then
  569. if [[ ! -s ${_arg_output_dir}/dbm/jacobian/final-target/${type}/smooth/$(basename ${file} | extension_strip)_fwhm_${fwhm}.nii.gz ]]; then
  570. echo SmoothImage 3 \
  571. ${_arg_output_dir}/dbm/jacobian/final-target/${type}/$(basename ${file} | extension_strip).nii.gz \
  572. ${sigma_num} \
  573. ${_arg_output_dir}/dbm/jacobian/final-target/${type}/smooth/$(basename ${file} | extension_strip)_fwhm_${fwhm}.nii.gz ${fwhm_type} 0
  574. fi
  575. fi
  576. done
  577. done
  578. done >${_arg_output_dir}/dbm/jobs/${__datetime}/smooth_jacobian
  580. debug "$(cat ${_arg_output_dir}/dbm/jobs/${__datetime}/smooth_jacobian)"
  581. if [[ ${_arg_dry_run} == "off" ]]; then
  582. qbatch ${_arg_block} --logdir ${_arg_output_dir}/dbm/logs/${__datetime} \
  583. --walltime ${_arg_walltime} \
  584. -N ${_arg_jobname_prefix}dbm_${__datetime}_smooth_jacobian \
  585. --depend ${_arg_jobname_prefix}dbm_${__datetime}_gen_full_jacobian \
  586. --depend ${_arg_jobname_prefix}dbm_${__datetime}_gen_rel_jacobian \
  587. --depend ${_arg_jobname_prefix}dbm_${__datetime}_resample_jacobians_final_target \
  588. ${_arg_output_dir}/dbm/jobs/${__datetime}/smooth_jacobian
  589. fi
  592. # ] <-- needed because of Argbash

dbm.sh at commit 477735b, under other · at the source

Overview

Authors: Kristina Zhang1,2, Jurgen Germann3, Rafi Matin1,2, Karim Mithani2,4, Jacob Ellegood5,6, Hrishikesh Suresh2,4, Sammi Wong5, Jason P Lerch5,7,8, Brian J Nieman5,7,9, Margot J Taylor2,10,11,12, Sara Breitbart4, Alfonso Fasano1,3, Carolina Gorodetsky13, Flavia Venetucci Gouveia2,5,9, George M Ibrahim1,2,4
ORCID iDs: Kristina Zhang, Jurgen Germann, Karim Mithani, Jacob Ellegood, Hrishikesh Suresh, Sammi Wong, Brian J Nieman, Margot J Taylor, Sara Breitbart, Alfonso Fasano, Carolina Gorodetsky, Flavia Venetucci Gouveia, George M Ibrahim
13 affiliations
  1. Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
  2. Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
  3. Krembil Brain Institute, University Health Network, Toronto, Ontario, Canada
  4. Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada
  5. Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
  6. Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
  7. Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
  8. Oxford Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
  9. Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
  10. Diagnostic and Interventional Radiology, The Hospital for Sick Children, Toronto, Ontario, Canada
  11. Department of Medical Imaging, University of Toronto, Toronto, Ontario, Canada
  12. Department of Psychology, University of Toronto, Toronto, Ontario, Canada
  13. Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
Institutions: University of Toronto (Canada); Hospital for Sick Children (Canada); University Health Network (Canada); Krembil Brain Institute; Holland Bloorview Kids Rehabilitation Hospital (Canada); Bloorview Research Institute (Canada); University of Oxford (United Kingdom); Wellcome Centre for Integrative Neuroimaging (United Kingdom)
Journal: Science advances, volume 12, issue 15, article eaeb5842
Dates: received 18 August 2025; accepted 11 March 2026; published online 10 April 2026; in print April 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1126/sciadv.aeb5842 · PMID 41961929 · PMCID PMC13068066 · OpenAlex W7153175071
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), mouse (organism), autism (population), systems (subfield)
Methods: Statistics, Connectivity, fMRI & imaging
MeSH: Autism Spectrum Disorder*, Autistic Disorder*, Cerebral Cortex*, Corpus Striatum*, Deep Brain Stimulation*, Self-Injurious Behavior*, Animals, Child, Disease Models, Animal, Electric Stimulation, Female, Humans, Male, Mice, Nucleus Accumbens (* major topic)
Topic: Transcranial Magnetic Stimulation Studies (Neurology, Neuroscience), according to OpenAlex
Funding: Garry Hurvitz Centre for Brain and Mental Health
Citations: cited by 1 paper (Europe PMC); 146 references in the paper

Abstract

Dysfunction of corticostriatal circuitry is related to the emergence of self-injurious behavior (SIB) in autism spectrum disorder (ASD). Despite mounting interest in circuit-based interventions for severe, refractory SIB, the lack of causal evidence linking modulation of corticostriatal networks to changes in SIB has limited the advancement of effective, targeted therapies. In this study, we demonstrate that electrical stimulation of the nucleus accumbens (NAcc) mitigates SIB and induces structural changes along corticostriatal circuits in a mouse model relevant for ASD and children with severe SIB undergoing NAcc-targeted deep brain stimulation. In BTBR T+ Itpr3tf/J mice, NAcc stimulation selectively reduced injurious self-grooming—a behavioral metric of SIB—and led to morphological changes in corticostriatal networks. In children with severe SIB, electric stimulation at a locus of optimal therapeutic response within the NAcc engaged widespread sensorimotor, limbic, and striatal networks and induced longitudinal structural changes in fronto-limbic-striatal brain regions. These findings highlight the role of the fronto-limbic-striatal network in SIB regulation and support corticostriatal neuromodulation as a mechanistic therapy for these extreme behaviors.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

lead-dbs.org

License: none: the authors keep all their rights
State: the link answers, verified on 26 September 2026
Evidence: the link answers
Software Heritage: not checked
Found in: “Data, code, and materials availability:”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 26 September 2026: the link answers (HTTP 200)
  • 26 September 2026: the link answers (HTTP 200)
At the source: lead-dbs.org/

CoBrALab/twolevel_ants_dbm

License: other
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: c51e45ac513106b03bdaac61aca58d60c51bba64, 16 May 2025
Languages: Python (1)
Size: 6 files, 1 script
Software Heritage: not archived
Found in: “Data, code, and materials availability:”
Holds: README, license file, CITATION.cff, environment (requirements.txt)
Not found: tests, continuous integration, documentation
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
3 files
At the source: github.com/CoBrALab/twolevel_ants_dbm

CoBrALab/optimized_antsMultivariateTemplateConstruction

License: other
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 477735b38736f9ba91f7e6372ab8eb77d8629bed, 21 September 2026
Languages: Shell (10), Python (4)
Size: 25 files, 14 scripts
Software Heritage: not archived
Found in: “Data, code, and materials availability:”
Holds: README, license file, CITATION.cff, documentation
Not found: environment file, tests, continuous integration
Tools: SimpleITK (4 files), NumPy (3 files), ANTs (2 files), SciPy (2 files), statsmodels (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
16 files
At the source: github.com/CoBrALab/optimized_antsMultivariateTemplateConstruction

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 3 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 15 scripts, each with its path and the digest of its content;
  • 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Data, code, and materials availability

All data and code needed to evaluate and reproduce the results in the paper are present in the paper and/or the Supplementary Materials. Code for electrode localization, modeling of the volume of activated tissue, and imaging connectomics are freely available in Lead-DBS (https://lead-dbs.org/). Structural (https://doi.org/10.1038/s41597-024-03197-0) and functional (https://doi.org/10.7910/DVN/KKTJQC) connectomes are publicly available. The code used for data-processing and human deformation-based morphometry analysis are available at http://dx.doi.org/10.52294/001c.133510, https://github.com/CoBrALab/twolevel_ants_dbm, and https://github.com/CoBrALab/optimized_antsMultivariateTemplateConstruction. This study did not generate new materials.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 15 authors, 15 MeSH terms, 1 funder, 141 references.

Cite

This paper

Zhang, K., Germann, J., Matin, R., Mithani, K., Ellegood, J., Suresh, H., Wong, S., Lerch, J. P., Nieman, B. J., Taylor, M. J., Breitbart, S., Fasano, A., Gorodetsky, C., Gouveia, F. V., & Ibrahim, G. M. (2026). Regulation of autism-related self-injurious behavior by electrical stimulation of corticostriatal circuits in mice and humans. Science advances, 12(15), eaeb5842. https://doi.org/10.1126/sciadv.aeb5842

BibTeX

@article{zhang2026regulation,
author = {Zhang, Kristina and Germann, Jurgen and Matin, Rafi and Mithani, Karim and Ellegood, Jacob and Suresh, Hrishikesh and Wong, Sammi and Lerch, Jason P and Nieman, Brian J and Taylor, Margot J and Breitbart, Sara and Fasano, Alfonso and Gorodetsky, Carolina and Gouveia, Flavia Venetucci and Ibrahim, George M},
title = {{Regulation of autism-related self-injurious behavior by electrical stimulation of corticostriatal circuits in mice and humans}},
journal = {Science advances},
year = {2026},
month = apr,
volume = {12},
number = {15},
pages = {eaeb5842},
publisher = {American Association for the Advancement of Science},
issn = {2375-2548},
doi = {10.1126/sciadv.aeb5842},
url = {https://doi.org/10.1126/sciadv.aeb5842},
pmid = {41961929},
pmcid = {PMC13068066}
}

RIS

TY - JOUR
AU - Zhang, Kristina
AU - Germann, Jurgen
AU - Matin, Rafi
AU - Mithani, Karim
AU - Ellegood, Jacob
AU - Suresh, Hrishikesh
AU - Wong, Sammi
AU - Lerch, Jason P
AU - Nieman, Brian J
AU - Taylor, Margot J
AU - Breitbart, Sara
AU - Fasano, Alfonso
AU - Gorodetsky, Carolina
AU - Gouveia, Flavia Venetucci
AU - Ibrahim, George M
TI - Regulation of autism-related self-injurious behavior by electrical stimulation of corticostriatal circuits in mice and humans
T2 - Science advances
J2 - Sci Adv
PY - 2026
DA - 2026/04/10
VL - 12
IS - 15
SP - eaeb5842
SN - 2375-2548
PB - American Association for the Advancement of Science
DO - 10.1126/sciadv.aeb5842
UR - https://doi.org/10.1126/sciadv.aeb5842
LA - en
ER -

CSL-JSON

{
"id": "10.1126/sciadv.aeb5842",
"type": "article-journal",
"title": "Regulation of autism-related self-injurious behavior by electrical stimulation of corticostriatal circuits in mice and humans",
"container-title": "Science advances",
"author": [
{
"family": "Zhang",
"given": "Kristina"
},
{
"family": "Germann",
"given": "Jurgen"
},
{
"family": "Matin",
"given": "Rafi"
},
{
"family": "Mithani",
"given": "Karim"
},
{
"family": "Ellegood",
"given": "Jacob"
},
{
"family": "Suresh",
"given": "Hrishikesh"
},
{
"family": "Wong",
"given": "Sammi"
},
{
"family": "Lerch",
"given": "Jason P"
},
{
"family": "Nieman",
"given": "Brian J"
},
{
"family": "Taylor",
"given": "Margot J"
},
{
"family": "Breitbart",
"given": "Sara"
},
{
"family": "Fasano",
"given": "Alfonso"
},
{
"family": "Gorodetsky",
"given": "Carolina"
},
{
"family": "Gouveia",
"given": "Flavia Venetucci"
},
{
"family": "Ibrahim",
"given": "George M"
}
],
"container-title-short": "Sci Adv",
"volume": "12",
"issue": "15",
"page": "eaeb5842",
"DOI": "10.1126/sciadv.aeb5842",
"PMID": "41961929",
"PMCID": "PMC13068066",
"ISSN": "2375-2548",
"publisher": "American Association for the Advancement of Science",
"URL": "https://doi.org/10.1126/sciadv.aeb5842",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
10
]
]
}
}

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In common: ANTs, statsmodels, SciPy, 1 other tool, systems, 2 references
[10] doi:10.1002/ana.78206 [code]
Multimodal Image Guidance in Subthalamic Deep Brain Stimulation for Parkinson's Disease.
Journal: Annals of neurology
In common: ANTs, SciPy, NumPy, 3 references

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