OSCR

Same ages, different stages: Pubertal development in 9- and 10-year olds is associated with entropy of fMRI signals.

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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.

The 2 matches
  1. [1] § Method › Measures › Sample entropy ↔ app/pipelines.py, lines 12–92 · score 0.67 · bandpass filter, 0.009 Hz, smoothing, DCANBOLDproc, surface, HCP
  2. [2] § Method › Measures › Sample entropy ↔ app/pipelines.py, lines 12–92 · score 0.65 · BOLD signal, vertex, motion, contiguity, FD, subcortical

Paper

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The authors' code

Python · 1,034 lines · 37 KB · BSD-3-Clause · 2 matches

  1. import inspect
  2. import json
  3. import multiprocessing as mp
  4. import subprocess
  6. import os
  8. from helpers import (get_fmriname, get_readoutdir, get_realdwelltime,
  9. get_relpath, get_taskname, ijk_to_xyz)
  12. class ParameterSettings(object):
  13. """
  14. Paths to files and settings required to run DCAN HCP. Class attributes
  15. should be any parameters which are independent of input image parameters,
  16. for example, the target atlases. Instance attributes are attributes which
  17. are read from or dependent upon inputs. Additionally, they may include
  18. special options for processing or for overriding class attributes. All
  19. attributes will be formatted according to the available
  20. """
  22. summary_dir = "summary_{DCANBOLDPROCVER}"
  24. # @ templates @ #
  25. # MNI0.7mm template
  26. t1template = "{HCPPIPEDIR_Templates}/MNI152_T1_1mm.nii.gz"
  27. # Brain extracted MNI0.7mm template
  28. t1templatebrain = "{HCPPIPEDIR_Templates}/MNI152_T1_1mm_brain.nii.gz"
  29. # MNI2mm template
  30. t1template2mm = "{HCPPIPEDIR_Templates}/MNI152_T1_2mm.nii.gz"
  31. # MNI0.7mm T2wTemplate
  32. t2template = "{HCPPIPEDIR_Templates}/MNI152_T2_1mm.nii.gz"
  33. # Brain extracted MNI0.7mm T2wTemplate
  34. t2templatebrain = "{HCPPIPEDIR_Templates}/MNI152_T2_1mm_brain.nii.gz"
  35. # MNI2mm T2wTemplate
  36. t2template2mm = "{HCPPIPEDIR_Templates}/MNI152_T2_2mm.nii.gz"
  37. # Brain mask MNI0.7mm template
  38. templatemask = "{HCPPIPEDIR_Templates}/MNI152_T1_1mm_brain_mask.nii.gz"
  39. # MNI2mm template
  40. template2mmmask = "{HCPPIPEDIR_Templates}/MNI152_T1_2mm_brain_mask_dil" \
  41. ".nii.gz"
  42. # Myelin Maps
  43. refmyelinmaps = "{HCPPIPEDIR_Templates}/standard_mesh_atlases/" \
  44. "Conte69.MyelinMap_BC.164k_fs_LR.dscalar.nii"
  45. # Surface Atlas Templates
  46. surfatlasdir = "{HCPPIPEDIR_Templates}/standard_mesh_atlases"
  47. # Grayordinate Templates
  48. grayordinatesdir = "{HCPPIPEDIR_Templates}/91282_Greyordinates"
  50. # @ various settings @ #
  51. # fov size for robust_fov automatic cropping
  52. brainsize = 150
  53. # final time series isotropic resolution (mm)
  54. fmrires = 2.0
  55. # resolution of greyordinates (mm)
  56. grayordinatesres = 2
  57. # smoothing sigma for final greyordinate data (mm)
  58. smoothingFWHM = 2
  59. # surface registration algorithm, one of: FS, MSMSulc
  60. regname = "MSMSulc"
  61. # number of vertices (in thousands) for high and low res surface meshes
  62. hiresmesh = "164"
  63. lowresmesh = "32"
  64. # motion correction method
  65. mctype = 'MCFLIRT'
  67. # @ configuration files @ #
  68. topupconfig = "{HCPPIPEDIR_Config}/b02b0.cnf"
  69. fnirtconfig = "{HCPPIPEDIR_Config}/T1_2_MNI152_2mm.cnf"
  70. freesurferlabels = "{HCPPIPEDIR_Config}/FreeSurferAllLut.txt"
  71. subcortgraylabels = "{HCPPIPEDIR_Config}/FreeSurferSubcortical" \
  72. "LabelTableLut.txt"
  74. # @ bold processing defaults @ #
  75. # brain radius of subject set
  76. brain_radius = 50
  77. # threshold for valid signal regression frames.
  78. fd_threshold = 0.3
  79. # bold signal temporal bandpass filter parameters
  80. filter_order = 2
  81. lower_bpf = 0.009
  82. upper_bpf = 0.080
  83. # motion regressor bandstop filter parameters
  84. motion_filter_type = 'notch'
  85. motion_filter_order = 4
  86. band_stop_min = None
  87. band_stop_max = None
  88. motion_filter_option = 5
  89. # seconds to omit from beginning of scan
  90. skip_seconds = 5
  91. # cont frames
  92. contiguous_frames = 5
  94. def __init__(self, bids_data, output_directory):
  95. """
  96. Specification to run pipeline on a single subject session.
  97. :param bids_data: yielded spec from read_bids_dataset
  98. :param output_directory: output directory for pipeline
  99. """
  101. # input bids data struct
  102. self.bids_data = bids_data
  103. # @ parameters read from bids @ #
  104. self.t1w = self.bids_data['t1w']
  105. self.t1samplespacing = get_realdwelltime(
  106. self.bids_data['t1w_metadata'])
  108. if 'T2w' in self.bids_data['types']:
  109. self.useT2 = 'true'
  110. self.t2w = self.bids_data['t2w']
  111. self.t2samplespacing = get_realdwelltime(
  112. self.bids_data['t2w_metadata'])
  113. else:
  114. self.useT2 = 'false'
  115. self.t2w = []
  116. self.t2samplespacing = None
  118. # distortion correction method: TOPUP, FIELDMAP, or NONE, inferred
  119. # from files, defaults to spin echo (topup) if both field maps exist
  120. self.unwarpdir = get_readoutdir(self.bids_data['t1w_metadata'])
  121. fmap_types = {'magnitude', 'magnitude1', 'magnitude2', 'phasediff',
  122. 'phase1', 'phase2', 'fieldmap'}
  123. if 'epi' in self.bids_data['types']:
  124. self.dcmethod = 'TOPUP'
  125. # spin echo field map spacing @TODO read during volume per fmap?
  126. self.echospacing = self.bids_data['fmap_metadata']['positive'][0][
  127. 'EffectiveEchoSpacing']
  128. self.echospacing = ('%.12f' % self.echospacing).rstrip('0')
  129. # distortion correction phase encoding direction
  130. # somewhat arbitrary in PreFreeSurfer
  131. if self.bids_data['func']:
  132. # take phase encoding direction from first functional.
  133. self.seunwarpdir = ijk_to_xyz(
  134. self.bids_data['func_metadata'][0]['PhaseEncodingDirection'])
  135. else:
  136. # if no functional data is provided, use positive spin echo
  137. self.seunwarpdir = ijk_to_xyz(
  138. self.bids_data['fmap_metadata']['positive'][0][
  139. 'PhaseEncodingDirection'])
  141. # set unused fmap parameters to none
  142. self.fmapmag = self.fmapphase = self.fmapgeneralelectric = \
  143. self.echodiff = self.gdcoeffs = None
  145. elif fmap_types.intersection(set(self.bids_data['types'])):
  146. self.dcmethod = 'FIELDMAP'
  147. types = self.bids_data['fmap'].keys()
  148. # gradient field map delta TE
  149. if 'magnitude1' in types and 'magnitude2' in types:
  150. self.fmapmag = self.bids_data['fmap']['magnitude1']
  151. self.echodiff = self.bids_data['fmap_metadata'][
  152. 'magnitude2']['EchoTime'] - self.bids_data[
  153. 'fmap_metadata']['magnitude1']['EchoTime']
  154. self.echodiff = '%g' % (self.echodiff * 1000.) # milliseconds
  155. self.fmapgeneralelectric = None
  156. elif 'magnitude' in types:
  157. raise NotImplementedError
  158. else:
  159. raise Exception('No FM magnitude image identified')
  161. if 'phasediff' in types:
  162. self.fmapphase = self.bids_data['fmap']['phasediff']
  163. elif 'phase1' in types and 'phase2' in types:
  164. raise NotImplementedError
  165. else:
  166. raise Exception('No FM phase image identified')
  167. # set unused spin echo parameters to none
  168. self.seunwarpdir = self.gdcoeffs = self.echospacing = None
  170. else:
  171. # all distortion correction parameters set to none
  172. self.fmapmag = self.fmapphase = self.fmapgeneralelectric = \
  173. self.echodiff = self.gdcoeffs = self.dcmethod = \
  174. self.seunwarpdir = self.echospacing = None
  176. if not hasattr(self, 'fmribfcmethod'):
  177. self.fmribfcmethod = None # this parameter has not been validated
  179. # dwi parameters
  180. if 'dwi' in self.bids_data['types']:
  181. pass
  183. # @TODO handle bids formatted physio data
  184. self.physio = None
  186. # intermediate template defaults
  187. self.usestudytemplate = "false"
  188. self.studytemplate = None
  189. self.studytemplatebrain = None
  191. # @ output files @ #
  192. self.path = os.path.join(output_directory, 'files')
  193. self.logs = os.path.join(output_directory, 'logs')
  194. self.subject = self.bids_data['subject']
  195. self.session = self.bids_data['session']
  197. # Exec summ doesn't need this anymore. KJS 11/6/18
  198. #deriv_root = self.path.split('/')[:-3]
  199. #self.deriv = '/'.join(deriv_root)
  201. # @ input files @ #
  202. session_root = '/'.join(self.t1w[0].split('/')[:-2])
  203. self.unproc = os.path.join(session_root, 'func')
  205. bids_input_root = '/'.join(session_root.split('/')[:-2])
  206. self.sourcedata_root = os.path.join(bids_input_root,'sourcedata')
  208. # print command for HCP
  209. self.printcom = ''
  211. def __getitem__(self, item):
  212. # item getter
  213. return self._params()[item]
  215. def __setitem__(self, key, value):
  216. # item setter
  217. setattr(self, key, value)
  219. def _params(self):
  220. """
  221. gets all class parameters which do not start with an underscore.
  222. :return: dictionary of class parameter names and values.
  223. """
  224. params = inspect.getmembers(self, lambda a: not inspect.isroutine(a))
  225. params = {x[0]: x[1] for x in params if not x[0].startswith('_')}
  226. return params
  228. def _format(self):
  229. """
  230. formats all class parameter strings to insert environment variables.
  231. :return: None
  232. """
  233. params = self._params()
  234. # format all attributes
  235. for item, value in params.items():
  236. if isinstance(value, str):
  237. setattr(self, item, value.format(**os.environ))
  239. def get_params(self):
  240. """
  241. formats and returns instance variables.
  242. :return: dictionary of instance variable names and values
  243. """
  244. self._format()
  245. return self._params()
  247. def get_bids(self, *args):
  248. """
  249. get data from bids struct
  250. :param args: list of nested dict keys, e.g. one must provide 'fmap',
  251. 'positive' to retrieve the positive spin echo field maps.
  252. :return: bids data
  253. """
  254. val = self.bids_data
  255. for arg in args:
  256. val = val[arg]
  257. return val
  259. def set_anat_only(self, anat_only=False):
  260. if anat_only:
  261. # Assume there is no 'func' data...
  262. self.unproc = None
  263. # and no output from dcan-bold-proc.
  264. self.summary_dir = None
  266. def set_study_template(self, study_template, study_template_brain):
  267. """
  268. set template for intermediate registration steps.
  269. :param study_template: intermediate registration template head.
  270. :param study_template_brain: intermediate registration template brain.
  271. :return: None
  272. """
  273. self.usestudytemplate = "true"
  274. self.studytemplate = study_template
  275. self.studytemplatebrain = study_template_brain
  277. def set_dcmethod(self, value):
  278. if value:
  279. self.dcmethod = value
  282. class Status(object):
  283. """Status provides and updates node status information.
  285. Status information for each node is stored in the
  286. processing_logs/NodeName/status.json file. This class provides an
  287. abstraction layer between the NodeStep class and this status file.
  289. This is a write through data structure
  290. """
  291. name = 'status.json'
  292. states = {
  293. 'unchecked': 999,
  294. 'not_started': 4,
  295. 'failed': 3,
  296. 'incomplete': 2,
  297. 'succeeded': 1,
  298. }
  300. def __init__(self, folder_path):
  301. """
  302. param folder_path (str): absolute path to the Stage's bookkeeping
  303. (e.g. /output/sub/ses/processing_logs/PipelineStage)
  304. """
  305. self.file_path = os.path.join(folder_path, Status.name)
  307. defaults = {
  308. 'num_runs': 0,
  309. 'node_status': Status.states['not_started'],
  310. 'comment': '',
  311. }
  313. if not os.path.exists(self.file_path):
  314. self._write_dict(**defaults)
  316. def __getitem__(self, key):
  317. # item getter
  318. with open(self.file_path, 'r') as fd:
  319. return json.load(fd)[key]
  321. def __setitem__(self, key, value):
  322. # item setter
  323. with open(self.file_path, 'r') as fd:
  324. store = json.load(fd)
  325. store[key] = value
  326. self._write_dict(**store)
  327. return value
  329. def _write_dict(self, **contents):
  330. """
  331. write status dictionary to status.json in Stage log folder.
  332. """
  333. with open(self.file_path, 'w') as fd:
  334. json.dump(contents, fd, indent=4)
  336. def increment_run(self):
  337. # tic runs up, should be called on stage start.
  338. self['num_runs'] += 1
  340. def update_start_run(self):
  341. # reset node_status to incomplete when stage begins
  342. self.increment_run()
  343. self['node_status'] = Status.states['incomplete']
  345. def update_success(self):
  346. # update successful completion of stage
  347. self['node_status'] = Status.states['succeeded']
  348. self['comment'] = ''
  350. def update_failure(self, comment=''):
  351. """
  352. update stage failed.
  353. :param comment: optional comment describing failure.
  354. """
  355. self['node_status'] = Status.states['failed']
  356. self['comment'] = comment
  358. def update_unchecked(self, comment='no expected_outputs list for '
  359. 'completed node'):
  360. # update no configured expected outputs: ambiguous success.
  361. self['node_status'] = Status.states['unchecked']
  362. self['comment'] = comment
  364. def succeeded(self):
  365. """
  366. returns boolean if stage successful or if ambiguous (no expected
  367. outputs configured)
  368. """
  369. return self['node_status'] in (Status.states['succeeded'],
  370. Status.states['unchecked'])
  373. class Stage(object):
  374. """
  375. Base abstract class for pipeline stages.
  377. attributes:
  378. config: ParameterSettings object.
  379. kwargs: dict of attributes returned from ParamterSettings object.
  381. abstract methods which require overriding:
  382. script: script / tool / executable to run as a subprocess.
  383. args: should provide command line arguments to the script. Usually
  384. utilizes a "spec" attribute which is then formatted with the "kwargs"
  385. attribute. See PreFreeSurfer. Must be a generator for concurrency. See
  386. FMRIVolume.
  388. optional overriding:
  389. cmdline: will need overriding as generator to utilize concurrency. See
  390. FMRIVolume.
  391. setup: executes prior to executable. Recommended to wrap super().
  392. teardown: executes after executable completes. Recommended to wrap super().
  394. run: not intended for override.
  395. """
  397. # runtime settings
  398. call_active = True
  399. check_expected_outputs_active = True
  400. remove_expected_outputs_active = True
  401. ignore_expected_outputs = False
  403. def __init__(self, config):
  404. """
  405. :param config: instance of ParameterSettings
  406. """
  407. self.config = config
  408. self.kwargs = config.get_params()
  409. self.status = Status(self._get_log_dir())
  410. here = os.path.dirname(os.path.realpath(__file__))
  411. with open(os.path.join(here, 'pipeline_expected_outputs.json')) as fd:
  412. jso = json.load(fd)
  413. self.expected_outputs_spec = jso[self.__class__.__name__]
  415. def __str__(self):
  416. cmdline = self.cmdline()
  417. if inspect.isgenerator(cmdline):
  418. string = ''
  419. for cmd in cmdline:
  420. string += ' \\\n '.join(cmd.split()) + '\n'
  421. else:
  422. string = ' \\\n '.join(cmdline.split())
  423. return string
  425. @classmethod
  426. def deactivate_runtime_calls(cls):
  427. # prevent stages (all subclasses) from executing subprocesses
  428. cls.call_active = False
  430. @classmethod
  431. def deactivate_check_expected_outputs(cls):
  432. # prevent stages (all subclasses) from checking expected outputs
  433. cls.check_expected_outputs_active = False
  435. @classmethod
  436. def deactivate_remove_expected_outputs(cls):
  437. # prevent stages (all subclasses) from removing expected outputs
  438. cls.remove_expected_outputs_active = False
  440. @classmethod
  441. def activate_ignore_expected_outputs(cls):
  442. # stages will not terminate even if missing expected outputs
  443. cls.ignore_expected_outputs = True
  445. def _get_log_dir(self):
  446. """
  447. returns the subject's log directory for this stage
  448. :return: path to log directory
  449. """
  450. log_dir = os.path.join(self.kwargs['logs'], self.__class__.__name__)
  451. if not os.path.isdir(log_dir):
  452. os.makedirs(log_dir)
  453. return log_dir
  455. def check_expected_outputs(self):
  456. """
  457. checks the existence of the expected outputs for this stage.
  458. :return: True if all outputs exist, else False.
  459. """
  460. if not self.check_expected_outputs_active:
  461. return True
  463. outputs = self.get_expected_outputs()
  464. checklist = [os.path.exists(p) for p in outputs]
  465. if not all(checklist):
  466. print('missing expected outputs from %s' %
  467. self.__class__.__name__)
  468. dne_list = [f for i, f in enumerate(outputs) if not checklist[i]]
  469. for f in dne_list:
  470. print('file not found: %s' % f)
  471. if not self.ignore_expected_outputs:
  472. return False
  474. return True
  476. def get_expected_outputs(self):
  477. """
  478. formats and returns expected outputs. Must be overridden for
  479. expected outputs of concurrent executions.
  480. :return: formatted list of expected outputs
  481. """
  482. expected_outputs = [p.format(**self.kwargs)
  483. for p in self.expected_outputs_spec]
  484. expected_outputs += self.get_conditional_expected_outputs()
  485. return expected_outputs
  487. def get_conditional_expected_outputs(self):
  488. """
  489. this method includes any logic which needs to be used to determine
  490. if a file is an expected output, for example when different input
  491. modalities are utilized. Override this for individual stages to
  492. have contextually defined expected outputs.
  493. :return: list of any conditional expected outputs
  494. """
  495. return []
  497. def remove_expected_outputs(self):
  498. """
  499. removes expected outputs for this stage if they exist.
  500. :return: None
  501. """
  502. if not self.remove_expected_outputs:
  503. return
  504. outputs = self.get_expected_outputs()
  505. checklist = [os.path.isfile(p) for p in outputs]
  506. if any(checklist):
  507. print('found outputs from an earlier run of %s' %
  508. self.__class__.__name__)
  509. rm_list = [f for i, f in enumerate(outputs) if checklist[i]]
  510. for f in rm_list:
  511. print('removing %s' % f)
  512. os.remove(f)
  514. def setup(self):
  515. """
  516. runs prior to main script for this stage.
  517. :return: None
  518. """
  519. self.status.update_start_run()
  520. self.remove_expected_outputs()
  522. def teardown(self, result=0):
  523. """
  524. runs following the main script for this stage
  525. :param result: exit status or list of exit statuses for the main
  526. script.
  527. :return: None
  528. """
  529. if isinstance(result, list) and all(v == 0 for v in result):
  530. result = 0
  531. if result == 0:
  532. self.status.update_success()
  533. else:
  534. self.status.update_failure(
  535. 'stage terminated with exit code %s' % result
  536. )
  537. if not self.check_expected_outputs():
  538. self.status.update_failure(
  539. 'stage terminated, some required files were not created.'
  540. )
  541. # @TODO update status in case of missing expected outputs
  542. # finally, terminate pipeline in case of failure.
  543. if self.status['node_status'] != Status.states['succeeded']:
  544. raise Exception('error caught during stage: %s' %
  545. self.__class__.__name__)
  547. @property
  548. def args(self):
  549. """
  550. Formats the command line argument "spec", returning the full string of
  551. inputs to the main script. Must be overridden.
  552. :return: string of space separated command line arguments.
  553. """
  554. raise NotImplementedError
  556. @property
  557. def script(self):
  558. """
  559. formattable string for the path to the main script. Must be
  560. overridden.
  561. """
  562. raise NotImplementedError
  564. def cmdline(self):
  565. """
  566. returns the formatted string for the command to be called. Must
  567. be overridden as a generator object for concurrent execution.
  568. :return: command line string.
  569. """
  570. script = self.script.format(**os.environ)
  571. return ' '.join((script, self.args))
  573. def run(self, ncpus=1):
  574. """
  575. runs this stage
  576. :param ncpus: number of available cores for concurrent execution or
  577. for multithreaded computation.
  578. :return: None
  579. """
  580. self.setup()
  581. # a generator cmdline supports parallel execution
  582. if inspect.isgeneratorfunction(self.cmdline):
  583. cmdlist = []
  584. for cmd in self.cmdline():
  585. log_dir = self._get_log_dir()
  586. out_log = os.path.join(log_dir,
  587. self.kwargs['fmriname'] + '.out')
  588. err_log = os.path.join(log_dir,
  589. self.kwargs['fmriname'] + '.err')
  590. cmdlist.append((cmd, out_log, err_log))
  591. with mp.Pool(processes=ncpus) as pool:
  592. result = pool.starmap(self.call, cmdlist)
  593. else:
  594. cmd = self.cmdline()
  595. log_dir = self._get_log_dir()
  596. out_log = os.path.join(log_dir, self.__class__.__name__ + '.out')
  597. err_log = os.path.join(log_dir, self.__class__.__name__ + '.err')
  598. result = self.call(cmd, out_log, err_log, num_threads=ncpus)
  599. self.teardown(result)
  601. def call(self, *args, **kwargs):
  602. """
  603. runs command if call is active.
  604. """
  605. if self.call_active:
  606. return _call(*args, **kwargs)
  607. else:
  608. return 0 # "success"
  611. class PreFreeSurfer(Stage):
  613. script = '{HCPPIPEDIR}/PreFreeSurfer/PreFreeSurferPipeline.sh'
  615. spec = ' --path={path}' \
  616. ' --subject={subject}' \
  617. ' --t1={t1}' \
  618. ' --t2={t2}' \
  619. ' --t1template={t1template}' \
  620. ' --t1templatebrain={t1templatebrain}' \
  621. ' --t1template2mm={t1template2mm}' \
  622. ' --t2template={t2template}' \
  623. ' --t2templatebrain={t2templatebrain}' \
  624. ' --t2template2mm={t2template2mm}' \
  625. ' --templatemask={templatemask}' \
  626. ' --template2mmmask={template2mmmask}' \
  627. ' --brainsize={brainsize}' \
  628. ' --fnirtconfig={fnirtconfig}' \
  629. ' --fmapmag={fmapmag}' \
  630. ' --fmapphase={fmapphase}' \
  631. ' --fmapgeneralelectric={fmapgeneralelectric}' \
  632. ' --echodiff={echodiff}' \
  633. ' --SEPhaseNeg={sephaseneg}' \
  634. ' --SEPhasePos={sephasepos}' \
  635. ' --echospacing={echospacing}' \
  636. ' --seunwarpdir={seunwarpdir}' \
  637. ' --t1samplespacing={t1samplespacing}' \
  638. ' --t2samplespacing={t2samplespacing}' \
  639. ' --unwarpdir={unwarpdir}' \
  640. ' --gdcoeffs={gdcoeffs}' \
  641. ' --avgrdcmethod={dcmethod}' \
  642. ' --topupconfig={topupconfig}' \
  643. ' --useT2={useT2}' \
  644. ' --printcom={printcom}' \
  645. ' --useStudyTemplate={usestudytemplate}' \
  646. ' --StudyTemplate={studytemplate}' \
  647. ' --StudyTemplateBrain={studytemplatebrain}'
  649. def __init__(self, config):
  650. super(__class__, self).__init__(config)
  651. # modify t1/t2 inputs for spec
  652. self.kwargs['t1'] = '@'.join(self.kwargs.get('t1w'))
  653. self.kwargs['t2'] = '@'.join(self.kwargs.get('t2w', []))
  654. if self.kwargs['dcmethod'] == 'TOPUP':
  655. self.kwargs['sephasepos'], self.kwargs['sephaseneg'] = \
  656. self._get_intended_sefmaps()
  657. else:
  658. self.kwargs['sephasepos'] = self.kwargs['sephaseneg'] = None
  660. def _get_intended_sefmaps(self):
  661. """
  662. search for IntendedFor field from sidecar json, else give the first
  663. spin echo pair. @TODO Unfortunately, it will cause problems if someone
  664. includes the substring "T1w" in a spin echo sidecar name.
  665. :return: pair of spin echos, parallel
  666. """
  668. intended_idx = {}
  669. for direction in ['positive', 'negative']:
  670. for idx, sefm in enumerate(self.config.get_bids('fmap_metadata',
  671. direction)):
  672. intended_targets = sefm.get('IntendedFor', [])
  673. if 'T1w' in ' '.join(intended_targets):
  674. intended_idx[direction] = idx
  675. break
  676. else:
  677. if idx != 1:
  678. print('WARNING: the intended %s spin echo for anatomical '
  679. 'distortion correction is not explicitly defined in '
  680. 'the sidecar json.' % direction)
  681. intended_idx[direction] = 0
  683. return self.config.get_bids('fmap', 'positive', intended_idx[
  684. 'positive']), \
  685. self.config.get_bids('fmap', 'negative', intended_idx['negative'])
  687. @property
  688. def args(self):
  689. # None to NONE
  690. kw = {k: (v if v is not None else "NONE")
  691. for k, v in self.kwargs.items()}
  692. return self.spec.format(**kw)
  695. class FreeSurfer(Stage):
  697. script = '{HCPPIPEDIR}/FreeSurfer/FreeSurferPipeline.sh'
  699. spec = ' --subject={subject}' \
  700. ' --subjectDIR={freesurferdir}' \
  701. ' --t1={t1_restore}' \
  702. ' --t1brain={t1_restore_brain}' \
  703. ' --t2={t2_restore}' \
  704. ' --useT2={useT2}' \
  705. ' --printcom={printcom}'
  707. def __init__(self, config):
  708. super(__class__, self).__init__(config)
  709. self.kwargs['freesurferdir'] = os.path.join(
  710. self.kwargs['path'], 'T1w')
  711. self.kwargs['t1_restore'] = os.path.join(
  712. self.kwargs['freesurferdir'], 'T1w_acpc_dc_restore.nii.gz')
  713. self.kwargs['t1_restore_brain'] = os.path.join(
  714. self.kwargs['freesurferdir'], 'T1w_acpc_dc_restore_brain.nii.gz')
  715. self.kwargs['t2_restore'] = os.path.join(
  716. self.kwargs['freesurferdir'], 'T2w_acpc_dc_restore.nii.gz')
  718. @property
  719. def args(self):
  720. return self.spec.format(**self.kwargs)
  723. class PostFreeSurfer(Stage):
  725. script = '{HCPPIPEDIR}/PostFreeSurfer/PostFreeSurferPipeline.sh'
  727. spec = ' --path={path}' \
  728. ' --subject={subject}' \
  729. ' --surfatlasdir={surfatlasdir}' \
  730. ' --grayordinatesdir={grayordinatesdir}' \
  731. ' --grayordinatesres={grayordinatesres}' \
  732. ' --hiresmesh={hiresmesh}' \
  733. ' --lowresmesh={lowresmesh}' \
  734. ' --subcortgraylabels={subcortgraylabels}' \
  735. ' --freesurferlabels={freesurferlabels}' \
  736. ' --refmyelinmaps={refmyelinmaps}' \
  737. ' --regname={regname}' \
  738. ' --reference2mm={t1template2mm}' \
  739. ' --reference2mmmask={template2mmmask}' \
  740. ' --config={fnirtconfig}' \
  741. ' --useT2={useT2}' \
  742. ' --t1template={t1template}' \
  743. ' --t1templatebrain={t1templatebrain}' \
  744. ' --t1template2mm={t1template2mm}' \
  745. ' --t2template={t2template}' \
  746. ' --t2templatebrain={t2templatebrain}' \
  747. ' --t2template2mm={t2template2mm}' \
  748. ' --templatemask={templatemask}' \
  749. ' --template2mmmask={template2mmmask}' \
  750. ' --useStudyTemplate={usestudytemplate}' \
  751. ' --StudyTemplate={studytemplate}' \
  752. ' --StudyTemplateBrain={studytemplatebrain}' \
  753. ' --printcom={printcom}'
  755. def __init__(self, config):
  756. super(__class__, self).__init__(config)
  758. @property
  759. def args(self):
  760. return self.spec.format(**self.kwargs)
  763. class FMRIVolume(Stage):
  765. script = '{HCPPIPEDIR}/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh'
  767. spec = ' --path={path}' \
  768. ' --subject={subject}' \
  769. ' --fmriname={fmriname}' \
  770. ' --fmritcs={fmritcs}' \
  771. ' --fmriscout={fmriscout}' \
  772. ' --SEPhaseNeg={sephaseneg}' \
  773. ' --SEPhasePos={sephasepos}' \
  774. ' --fmapmag={fmapmag}' \
  775. ' --fmapphase={fmapphase}' \
  776. ' --fmapgeneralelectric={fmapgeneralelectric}' \
  777. ' --echospacing={echospacing}' \
  778. ' --echodiff={echodiff}' \
  779. ' --unwarpdir={seunwarpdir}' \
  780. ' --fmrires={fmrires}' \
  781. ' --dcmethod={dcmethod}' \
  782. ' --gdcoeffs={gdcoeffs}' \
  783. ' --topupconfig={topupconfig}' \
  784. ' --printcom={printcom}' \
  785. ' --biascorrection={fmribfcmethod}' \
  786. ' --mctype={mctype}' \
  787. ' --useT2={useT2}'
  789. def __init__(self, config):
  790. super(__class__, self).__init__(config)
  792. def __str__(self):
  793. string = ''
  794. for cmd in self.cmdline():
  795. string += ' \\\n '.join(cmd.split()) + '\n'
  796. return string
  798. def _get_intended_sefmaps(self):
  799. """
  800. search for IntendedFor field from sidecar json to determine
  801. appropriate field map pair, else give the first spin echo pair.
  802. :return: pair of spin echo filenames, positive then negative
  803. """
  804. intended_idx = {}
  805. for direction in ['positive', 'negative']:
  806. for idx, sefm in enumerate(self.config.get_bids('fmap_metadata',
  807. direction)):
  808. intended_targets = sefm.get('IntendedFor', [])
  809. if get_relpath(self.kwargs['fmritcs']) in ' '.join(
  810. intended_targets):
  811. intended_idx[direction] = idx
  812. break
  813. else:
  814. if idx != 0:
  815. print('WARNING: the intended %s spin echo for anatomical '
  816. 'distortion correction is not explicitly defined in '
  817. 'the sidecar json.' % direction)
  818. intended_idx[direction] = 0
  820. return self.config.get_bids('fmap', 'positive', intended_idx[
  821. 'positive']), \
  822. self.config.get_bids('fmap', 'negative',
  823. intended_idx['negative'])
  825. @property
  826. def args(self):
  827. for fmri, meta in zip(self.config.get_bids('func'),
  828. self.config.get_bids('func_metadata')):
  829. # set ts parameters
  830. self.kwargs['fmritcs'] = fmri
  831. self.kwargs['fmriname'] = get_fmriname(fmri)
  832. self.kwargs['fmriscout'] = None # not implemented
  833. if self.kwargs['dcmethod'] == 'TOPUP':
  834. self.kwargs['seunwarpdir'] = ijk_to_xyz(
  835. meta['PhaseEncodingDirection'])
  836. self.kwargs['sephasepos'], self.kwargs['sephaseneg'] = \
  837. self._get_intended_sefmaps()
  838. else:
  839. self.kwargs['sephasepos'] = self.kwargs['sephaseneg'] = None
  840. # None to NONE
  841. kw = {k: (v if v is not None else "NONE")
  842. for k, v in self.kwargs.items()}
  843. yield self.spec.format(**kw)
  845. def cmdline(self):
  846. script = self.script.format(**os.environ)
  847. for argset in self.args:
  848. yield ' '.join((script, argset))
  851. class FMRISurface(Stage):
  853. script = '{HCPPIPEDIR}/fMRISurface/GenericfMRISurfaceProcessingPipeline.sh'
  855. spec = ' --path={path}' \
  856. ' --subject={subject}' \
  857. ' --fmriname={fmriname}' \
  858. ' --lowresmesh={lowresmesh}' \
  859. ' --fmrires={fmrires}' \
  860. ' --smoothingFWHM={smoothingFWHM}' \
  861. ' --grayordinatesres={grayordinatesres}' \
  862. ' --regname={regname}'
  864. def __init__(self, config):
  865. super(__class__, self).__init__(config)
  867. def __str__(self):
  868. string = ''
  869. for cmd in self.cmdline():
  870. string += ' \\\n '.join(cmd.split()) + '\n'
  871. return string
  873. @property
  874. def args(self):
  875. for fmri in self.config.get_bids('func'):
  876. self.kwargs['fmriname'] = get_fmriname(fmri)
  877. yield self.spec.format(**self.kwargs)
  879. def cmdline(self):
  880. script = self.script.format(**os.environ)
  881. for argset in self.args:
  882. yield ' '.join((script, argset))
  885. class DCANBOLDProcessing(Stage):
  887. script = '{DCANBOLDPROCDIR}/dcan_bold_proc.py'
  889. spec = ' --subject={subject}' \
  890. ' --output-folder={path}' \
  891. ' --task={fmriname}' \
  892. ' --fd-threshold={fd_threshold}' \
  893. ' --filter-order={filter_order}' \
  894. ' --lower-bpf={lower_bpf}' \
  895. ' --upper-bpf={upper_bpf}' \
  896. ' --motion-filter-type={motion_filter_type}' \
  897. ' --physio={physio}' \
  898. ' --motion-filter-option={motion_filter_option}' \
  899. ' --motion-filter-order={motion_filter_order}' \
  900. ' --band-stop-min={band_stop_min}' \
  901. ' --band-stop-max={band_stop_max}' \
  902. ' --brain-radius={brain_radius}' \
  903. ' --skip-seconds={skip_seconds}' \
  904. ' --contiguous-frames={contiguous_frames}'
  906. def __init__(self, config):
  907. super(__class__, self).__init__(config)
  909. def set_bandstop_filter(self, lower_bound, upper_bound,
  910. filter_type='notch'):
  911. self.kwargs['motion_filter_type'] = filter_type
  912. self.kwargs['band_stop_min'] = lower_bound
  913. self.kwargs['band_stop_max'] = upper_bound
  915. def setup(self):
  916. """
  917. make ventricle and white matter masks.
  918. :return:
  919. """
  920. super(__class__, self).setup()
  921. script = self.script.format(**os.environ)
  922. args = self.spec.format(**self.kwargs)
  923. cmd = ' '.join((script, args))
  924. cmd += ' --setup'
  925. log_dir = self._get_log_dir()
  926. out_log = os.path.join(log_dir, self.__class__.__name__ + '_setup.out')
  927. err_log = os.path.join(log_dir, self.__class__.__name__ + '_setup.err')
  928. result = self.call(cmd, out_log, err_log)
  930. def teardown(self, result=0):
  931. """
  932. concatenate dtseries, parcellate, create grayplots.
  933. :param result:
  934. :return:
  935. """
  936. fmris = [get_fmriname(fmri) for fmri in self.config.get_bids('func')]
  937. fmrisets = list(set([get_taskname(fmri)
  938. for fmri in self.config.get_bids('func')]))
  940. script = self.script.format(**os.environ)
  941. args = self.spec.format(**self.kwargs)
  942. cmd = ' '.join((script, args))
  943. cmd += ' --teardown'
  945. for fmriset in fmrisets:
  946. fmrilist = sorted([fmri for fmri in fmris if fmriset in fmri])
  947. cmd += ' --tasklist ' + ','.join(fmrilist)
  949. log_dir = self._get_log_dir()
  950. out_log = os.path.join(log_dir, self.__class__.__name__ + '_teardown.out')
  951. err_log = os.path.join(log_dir, self.__class__.__name__ + '_teardown.err')
  952. result = self.call(cmd, out_log, err_log)
  954. super(__class__, self).teardown(result)
  956. @property
  957. def args(self):
  958. for fmri in self.config.get_bids('func'):
  959. self.kwargs['fmriname'] = get_fmriname(fmri)
  960. yield self.spec.format(**self.kwargs)
  962. def cmdline(self):
  963. script = self.script.format(**os.environ)
  964. for argset in self.args:
  965. yield ' '.join((script, argset))
  967. class DiffusionPreprocessing(Stage):
  969. script = '{HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh'
  971. spec = ' --path={path}' \
  972. ' --subject={subject}' \
  973. ' --posData={dwi_positive}' \
  974. ' --negData={dwi_negative}' \
  975. ' --echospacing={dwi_echospacing}' \
  976. ' --PEdir={pedir}' \
  977. ' --printcom={printcom}'
  979. @property
  980. def args(self):
  981. raise NotImplemented
  983. def cmdline(self):
  984. raise NotImplemented
  987. class ExecutiveSummary(Stage):
  989. script = '{EXECSUMDIR}/ExecutiveSummary.py'
  991. spec = ' --bids-input={unproc}' \
  992. ' --output-dir={path}' \
  993. ' --participant-label={subject}' \
  994. ' --session-id={session}' \
  995. ' --atlas={t1templatebrain}' \
  996. ' --dcan-summary={summary_dir} '
  998. def __init__(self, config):
  999. super(__class__, self).__init__(config)
  1001. @property
  1002. def args(self):
  1003. return self.spec.format(**self.kwargs)
  1006. class CustomClean(Stage):
  1008. script = '{CUSTOMCLEANDIR}/cleaning_script.py'
  1010. spec = ' --dir={path}' \
  1011. ' --json={input_json}'
  1013. def __init__(self, config, input_json):
  1014. super(__class__, self).__init__(config)
  1015. self.kwargs['input_json'] = input_json
  1017. @property
  1018. def args(self):
  1019. return self.spec.format(**self.kwargs)
  1022. def _call(cmd, out_log, err_log, num_threads=1):
  1023. env = os.environ.copy()
  1024. if num_threads > 1:
  1025. # set parallel environment variables
  1026. env['OMP_NUM_THREADS'] = str(num_threads)
  1027. env['ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS'] = str(num_threads)
  1028. with open(out_log, 'w') as out, open(err_log, 'w') as err:
  1029. result = subprocess.call(cmd.split(), stdout=out, stderr=err, env=env)
  1030. if type(result) is list:
  1031. if all(v == 0 for v in result):
  1032. result = 0
  1033. return result

pipelines.py at commit 0fe7f44, under BSD-3-Clause · at the source

Overview

Authors: Kirsten MP McKone1, Donovan J Roediger2, Stefanie L Sequeira3, Ellery Island4, Monica Luciana5, Mark B Fiecas4, Bryon A Mueller2, Bonnie Klimes-Dougan5, Kathryn R Cullen2
ORCID iDs: Kirsten MP McKone
  1. University of Minnesota Institute of Child Development, USA
  2. University of Minnesota Department of Psychiatry & Behavioral Sciences, USA
  3. University of Virginia Department of Psychology, USA
  4. University of Minnesota Division of Biostatistics, USA
  5. University of Minnesota Department of Psychology, USA
Institutions: University of Minnesota (United States); University of Virginia (United States)
Journal: Developmental cognitive neuroscience, volume 81, article 101806
Dates: received 5 March 2026; accepted 27 August 2026; published online 1 September 2026; in print September 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1016/j.dcn.2026.101806 · PMID 42691580 · PMCID PMC13571737 · OpenAlex W7204949848
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: fMRI (modality), human (organism), developmental (subfield)
Methods: Spectral & time-frequency, Statistics, Complexity, fMRI & imaging
Keywords: Entropy, Pubertal development, Adolescence, ABCD Study, Brain development, Complexity, RsFMRI BOLD signal
Topic: Hypothalamic control of reproductive hormones (Reproductive Medicine, Medicine), according to OpenAlex
Funding: NIDA NIH HHS (U01 DA050988, U01 DA050989, U01 DA051016, U01 DA051037, U01 DA051038, U01 DA041022, U01 DA041148, U01 DA050987, U01 DA041134, U01 DA041120, U01 DA041156, U01 DA041048, U01 DA041025, U01 DA041174, U01 DA041028, U01 DA041093, U01 DA041117, U01 DA051018, U24 DA041123, U01 DA041089, U01 DA041106, U01 DA051039, U24 DA041147); National Institutes of Health (U01DA050988, U01DA051039, U01DA041089, U01DA041117, U01DA041134, U01DA041048, U01DA041174, U01DA051018, U24DA041147, U01DA041025, U01DA041106, U01DA050987, U01DA051038, U01DA041028, U01DA041148, U01DA041156, U01DA041093, U01DA041120, U01DA051016, U24DA041123, U01DA041022, U01DA050989, U01DA051037); NIMH NIH HHS (R01 MH122473, T32 MH015755)
Citations: not cited yet (Europe PMC); 67 references in the paper

Abstract

Entropy is a novel brain measure that holds important information about brain flexibility and functioning, with promise for informing brain development in adolescence, as it has been shown to change across the lifespan. However, little is known about how it changes during the critically important phase of pubertal development, which kickstarts a period of broad neural reorganization and restructuring. This proof-of-concept cross-sectional study examined associations between fMRI signal entropy and early pubertal development in a large, diverse sample of children. Data (N = 6838; 49.6% male; ages 8.92–11.08) was drawn from the first wave of the Adolescent Brain Cognitive Development study. Sample entropy was calculated on the time series of the resting-state fMRI signals for every grayordinate (i.e., cortical vertex and subcortical voxel). Parent-reported pubertal development (approximated Tanner stage) and salivary hormone levels (dehydroepiandrosterone; estradiol; testosterone) were correlated with sample entropy across the whole brain. The patterns of association between sample entropy and pubertal stage/hormone levels were inspected for males and females separately. Findings indicated pubertal development was associated with higher levels of resting state fMRI signal entropy, specifically in the occipital, parietal, and temporal lobes. Associations were apparent in females across most pubertal metrics. For males the constrained range of pubertal development may in part account for weaker associations observed. Further, adjustment for variables associated with early timing of pubertal development (socioeconomic status, body mass index) reduced the strength of puberty-entropy associations for both sexes. Longitudinal research is needed to confirm the associations between sample entropy and puberty, to evaluate whether stronger associations emerge as more males enter puberty in earnest, and to disentangle potential confounds.

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

Repository

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

DCAN-Labs/abcd-hcp-pipeline

License: BSD-3-Clause
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 0fe7f449057b85eab9727d22a3302ce91499b86a, 16 January 2026
Languages: Python (4), Shell (2)
Size: 24 files, 6 scripts
Software Heritage: not archived
Found in: the text, “Data Statement”
Holds: README, license file, environment (Dockerfile, requirements.txt, app/requirements.txt), continuous integration, documentation
Not found: CITATION.cff, tests
Tools: FreeSurfer (2 files), FSL (1 file), HCP Pipelines (1 file), PyBIDS (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
8 files
At the source: github.com/DCAN-Labs/abcd-hcp-pipeline

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:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 6 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

No dataset and no data link were found in the paper.

Data availability

Data are publicly available at https://nda.nih.gov/abcd.

Reproduced under the paper's license (CC BY), 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, 27 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 9 authors, 7 keywords, 3 funders, 66 references.

Cite

This paper

McKone, K. M., Roediger, D. J., Sequeira, S. L., Island, E., Luciana, M., Fiecas, M. B., Mueller, B. A., Klimes-Dougan, B., & Cullen, K. R. (2026). Same ages, different stages: Pubertal development in 9- and 10-year olds is associated with entropy of fMRI signals. Developmental cognitive neuroscience, 81, 101806. https://doi.org/10.1016/j.dcn.2026.101806

BibTeX

@article{mckone2026same,
author = {McKone, Kirsten MP and Roediger, Donovan J and Sequeira, Stefanie L and Island, Ellery and Luciana, Monica and Fiecas, Mark B and Mueller, Bryon A and Klimes-Dougan, Bonnie and Cullen, Kathryn R},
title = {{Same ages, different stages: Pubertal development in 9- and 10-year olds is associated with entropy of fMRI signals}},
journal = {Developmental cognitive neuroscience},
year = {2026},
month = sep,
volume = {81},
pages = {101806},
publisher = {Elsevier},
issn = {1878-9293},
doi = {10.1016/j.dcn.2026.101806},
url = {https://doi.org/10.1016/j.dcn.2026.101806},
pmid = {42691580},
pmcid = {PMC13571737}
}

RIS

TY - JOUR
AU - McKone, Kirsten MP
AU - Roediger, Donovan J
AU - Sequeira, Stefanie L
AU - Island, Ellery
AU - Luciana, Monica
AU - Fiecas, Mark B
AU - Mueller, Bryon A
AU - Klimes-Dougan, Bonnie
AU - Cullen, Kathryn R
TI - Same ages, different stages: Pubertal development in 9- and 10-year olds is associated with entropy of fMRI signals
T2 - Developmental cognitive neuroscience
J2 - Dev Cogn Neurosci
PY - 2026
DA - 2026/09/01
VL - 81
SP - 101806
SN - 1878-9293
PB - Elsevier
DO - 10.1016/j.dcn.2026.101806
UR - https://doi.org/10.1016/j.dcn.2026.101806
LA - en
ER -

CSL-JSON

{
"id": "10.1016/j.dcn.2026.101806",
"type": "article-journal",
"title": "Same ages, different stages: Pubertal development in 9- and 10-year olds is associated with entropy of fMRI signals",
"container-title": "Developmental cognitive neuroscience",
"author": [
{
"family": "McKone",
"given": "Kirsten MP"
},
{
"family": "Roediger",
"given": "Donovan J"
},
{
"family": "Sequeira",
"given": "Stefanie L"
},
{
"family": "Island",
"given": "Ellery"
},
{
"family": "Luciana",
"given": "Monica"
},
{
"family": "Fiecas",
"given": "Mark B"
},
{
"family": "Mueller",
"given": "Bryon A"
},
{
"family": "Klimes-Dougan",
"given": "Bonnie"
},
{
"family": "Cullen",
"given": "Kathryn R"
}
],
"container-title-short": "Dev Cogn Neurosci",
"volume": "81",
"page": "101806",
"DOI": "10.1016/j.dcn.2026.101806",
"PMID": "42691580",
"PMCID": "PMC13571737",
"ISSN": "1878-9293",
"publisher": "Elsevier",
"URL": "https://doi.org/10.1016/j.dcn.2026.101806",
"language": "en",
"issued": {
"date-parts": [
[
2026,
9,
1
]
]
}
}

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