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Ultrasound neural interface enabling acute spinal cord monitoring and blood flow modulation

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  1. [1] § MATERIALS AND METHODS › Ultrasound imaging acquisition ↔ HEPIUS_MUSIC_imaging-main/matlab/SetUpL11_5vSpectralDoppler.m, lines 1 to 74 · score 0.83 · Vantage NXT, duplex mode, Doppler PRF, ultrasound system, spectral Doppler, Doppler image · Report a mismatch
  2. [2] § MATERIALS AND METHODS › Ultrasound imaging acquisition ↔ HEPIUS_MUSIC_imaging-main/matlab/SetupMusicSD_saveiq.m, lines 1 to 95 · score 0.75 · duplex mode, Doppler PRF, ultrasound system, Doppler image, spectral Doppler, pixel · Report a mismatch

Paper

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The authors' code

MATLAB · 868 lines · 33 KB · no license · 1 match

  1. %
  2. % File name: SetUpL11_5vSpectralDoppler.m - Spectral doppler with plane wave transmit.
  3. %
  4. % Description:
  5. % Sequence programming file for L11-5v Linear array, using plane wave
  6. % transmits for 2D and doppler imaging.
  7. % - for the 2D image, a single plane wave transmit is used. All transmit
  8. % and receive channels are active for each acquisition.
  9. % - for the doppler ensemble, multiple pulses are transmitted at a
  10. % steering angle of dopAngle radians. 128 transmit and 64 receive
  11. % channels are active for each acquisition. The Doppler measurement
  12. % region is the region under the central 64 transducer elements.
  13. % - processing is asynchronous with respect to acquisition
  14. % - An acquisition 'frame' consists of the number of transmit/receive events
  15. % that equals 10msec of time. Doppler and 2D acquisitions are interleaved.
  16. % - Doppler PRF will be quantized such that the acquisition PRF (twice
  17. % the Doppler PRF) has a PRI of integer microseconds.
  18. % - For the Doppler measurement, the sample volume in the measurement
  19. % region is selected by clicking the left mouse button in the DisplayWindow.
  20. % The sample volume is selected as a single I,Q pixel whose location is
  21. % indicated by a red circle. This action also switches the processing mode
  22. % to Doppler only. Clicking the right mouse button cancels the Doppler
  23. % processing and returns to 2D only processing. While the processing
  24. % operates in duplex mode - either 2D or Doppler, acquisition is always
  25. % the same, allowing Doppler operation in RcvData Loop playback mode.
  26. %
  27. % Notice:
  28. % This file is provided by Verasonics to end users as a programming
  29. % example for the Verasonics Vantage NXT Research Ultrasound System.
  30. % Verasonics makes no claims as to the functionality or intended
  31. % application of this program and the user assumes all responsibility
  32. % for its use.
  33. %
  34. % Copyright © 2013-2023 Verasonics, Inc.
  36. clear all
  38. % - 2D P(1) structure
  39. P(1).startDepth = 2; % Acquisition depth in wavelengths
  40. P(1).endDepth = 128; % This should preferrably be a multiple of 128 samples.
  41. % - Doppler P(2) structure (This is the pixel region for possible Doppler reconstructions.)
  42. P(2).startDepth = 0; % Acquisition depth in wavelengths
  43. P(2).endDepth = 128; % This should preferrably equate to a multiple of 128 samples.
  45. nfrms = 10; % no. of frames to acquire in RcvBuffer (sets size of RF cineloop).
  46. dopPRFnominal = 2000;
  47. framePeriodnominal_uSec = 40000; % nominal frame period for collections of PRIs.
  48. [psched ] = spectralDoppler('restrictAcqPRF',framePeriodnominal_uSec,dopPRFnominal);
  49. [pschedAll ]= spectralDoppler('restrictAcqPRF',framePeriodnominal_uSec,[]);
  50. disp(' '),
  51. disp([mfilename,': Allowed PRF values: '])
  52. disp(sprintf('%4.4f Hz\n',pschedAll.PRFDop))
  53. framePeriod = psched.FrameTime_uSec*1e-6;
  54. dopPRF = psched.PRFDop;
  55. ttna_microsec = psched.PRIAcq_uSec;
  56. acqPRF = psched.PRFAcq;
  57. maxAcqPRF = psched.maxPRFAcq;
  58. maxDopPRF = psched.maxPRFDop;
  59. minAcqPRF = psched.minPRFAcq;
  60. minDopPRF = psched.minPRFDop;
  61. NWindow = round(dopPRF*0.014); %samples in FFT window (not including zero padding)
  62. SDDespeckle = 0.4;
  63. dopWFCutoffNorm = 0.025; %allfilter normalized cutoff frequency
  64. dopSweepTimeIndex = 2;%1-4 avail for 20msec frame time
  65. SDDynRangeDB = 13;% not including FFT processing gain
  66. sgp= spectralDoppler('spectrogramParameters',framePeriod,dopSweepTimeIndex);
  67. sweepTime = sgp.THist;
  68. baseLineShiftNorm = -0.375;
  70. nPRIs = psched.pulsesPerFrameAcq; % needs to start as even .default no. of acquisition PRIs in a 'frame'
  71. nDopPRIs = psched.pulsesPerFrameDop;
  72. dopAngle = 14 * pi/180; % angle for Doppler flash transmits.
  74. maxPRIs = psched.pulsesPerFrameAcqMax ; % max no. of acquisition PRIs in a frame .
  76. % - Specify system parameters
  77. Resource.Parameters.numTransmit = 244; % number of transmit channels.
  78. Resource.Parameters.numRcvChannels = 244; % number of receive channels.
  79. Resource.Parameters.speedOfSound = 1540;
  80. Resource.Parameters.speedCorrectionFactor = 1.0;
  81. Resource.Parameters.initializeOnly = 0;
  82. Resource.Parameters.simulateMode = 0;
  83. Resource.Parameters.Connector = [1,2];
  85. % Specify Trans structure array.
  86. %Trans.name = 'L11-5v';
  87. Trans.name = 'MUSIC3_Biobox';
  88. Trans.units = 'wavelengths'; % Explicit declaration avoids warning message when selected by default
  89. Trans = computeTrans2(Trans); % computeTrans is used for known transducers.
  90. Trans.maxHighVoltage = 30; % set a reasonable high voltage limit.
  92. % Specify PData structure arrays.
  93. % - 2D PData structure
  94. PData(1).PDelta = [1.0,0,0.5];
  95. PData(1).Size(1,1) = ceil(P(1).endDepth/PData(1).PDelta(3)); % rows
  96. PData(1).Size(1,2) = ceil((Trans.numelements*Trans.spacing)/PData(1).PDelta(1)); % cols
  97. PData(1).Size(1,3) = 1; % single image page
  98. PData(1).Origin = [-Trans.spacing*(Trans.numelements-1)/2,0,P(1).startDepth]; % x,y,z of upr lft crnr w respect to xducer origin.
  99. % - Doppler PData structure
  100. PData(2).PDelta = [1.0,0,1.0];
  101. PData(2).Size(1,1) = 4; % 4 IQ samples for Doppler
  102. PData(2).Size(1,2) = 1; % single column for Doppler
  103. PData(2).Size(1,3) = 1; % single image page
  104. PData(2).Origin = [0,0,ceil(P(2).endDepth/2)];
  105. % - Region Outline for Region Constrain of Doppler Processing
  106. DopRegionLim.x = [-32,32]; % in wavelength
  107. DopRegionLim.y = [4,128];
  108. PData(3) = PData(1);
  109. PData(3).Region = struct('Shape',struct('Name','Rectangle',...
  110. 'Position',[0,0,DopRegionLim.y(1)],...
  111. 'width',diff(DopRegionLim.x),...
  112. 'height',diff(DopRegionLim.y)));
  114. % Specify Media object.
  115. pt1;
  116. Media.function = 'movePoints';
  118. % - RcvBuffer(1) is for 2D, and Doppler steering angle.
  119. Resource.RcvBuffer(1).datatype = 'int16';
  120. Resource.RcvBuffer(1).rowsPerFrame = 2048*maxPRIs;
  121. Resource.RcvBuffer(1).colsPerFrame = Resource.Parameters.numRcvChannels;
  122. Resource.RcvBuffer(1).numFrames = nfrms;
  123. % - InterBuffer(1) is for 2D data.
  124. Resource.InterBuffer(1).datatype = 'complex';
  125. Resource.InterBuffer(1).numFrames = 1; % one intermediate frame needed for 2D.
  126. % - InterBuffer(2) is for Doppler data.
  127. Resource.InterBuffer(2).datatype = 'complex';
  128. Resource.InterBuffer(2).numFrames = 1; % two intermediate frames needed for color
  129. Resource.InterBuffer(2).pagesPerFrame = maxPRIs/2; % no. of pages set by maxPRIs
  130. % - ImageBuffer(1) is for 2D image.
  131. Resource.ImageBuffer(1).datatype = 'double';
  132. Resource.ImageBuffer(1).numFrames = 10;
  133. % - DisplayWindow for 2D image
  134. Resource.DisplayWindow(1).Title = 'L11-5vSpectralDoppler';
  135. Resource.DisplayWindow(1).pdelta = 0.4;
  136. ScrnSize = get(0,'ScreenSize');
  137. DwWidth = ceil(PData(1).Size(2)*PData(1).PDelta(1)/Resource.DisplayWindow(1).pdelta);
  138. DwHeight = ceil(PData(1).Size(1)*PData(1).PDelta(3)/Resource.DisplayWindow(1).pdelta);
  139. Resource.DisplayWindow(1).Position = [250,(ScrnSize(4)-(DwHeight+150))/2, ... % lower left corner position
  140. DwWidth, DwHeight];
  141. Resource.DisplayWindow(1).ReferencePt = [PData(1).Origin(1),0,PData(1).Origin(3)]; % 2D imaging is in the X,Z plane
  142. Resource.DisplayWindow(1).numFrames = 20;
  143. Resource.DisplayWindow(1).Type = 'Verasonics';
  144. Resource.DisplayWindow(1).AxesUnits = 'mm';
  145. Resource.DisplayWindow(1).Colormap = gray(256);
  147. % Specify Transmit waveform structure.
  148. % - 2D transmit waveform
  149. TW(1).type = 'parametric';
  150. TW(1).Parameters = [Trans.frequency,0.67,2,1];
  151. % - Doppler transmit waveform
  152. TW(2).type = 'parametric';
  153. TW(2).Parameters = [Trans.frequency,0.67,6,1];
  155. % Specify TX structure arrays.
  156. % We need 1 TX specification for 2D and 1 TX specification for Doppler (1 steering angle).
  157. TX = repmat(struct('waveform', 1, ...
  158. 'Origin', [0.0,0.0,0.0], ...
  159. 'focus', 0.0, ...
  160. 'Steer', [0.0,0.0], ...
  161. 'Apod', ones(1,Trans.numelements), ...
  162. 'Delay', zeros(1,Trans.numelements)), 1, 2); %
  163. % - Set event specific TX attributes.
  164. TX(1).Delay = computeTXDelays(TX(1));
  165. % -- Second TX struct needed for Doppler
  166. TX(2).waveform = 2;
  167. TX(2).Steer = [dopAngle,0.0];
  168. TX(2).Delay = computeTXDelays(TX(2));
  170. % Specify TGC Waveform structures.
  171. % 2D TGC waveform
  172. TGC(1).CntrlPts = [51,331,430,515,603,690,777,887];
  173. TGC(1).rangeMax = P(1).endDepth;
  174. TGC(1).Waveform = computeTGCWaveform(TGC(1));
  175. % Doppler TGC waveform
  176. TGC(2).CntrlPts = [400,500,640,710,770,830,890,950];
  177. TGC(2).rangeMax = P(1).endDepth;
  178. TGC(2).Waveform = computeTGCWaveform(TGC(2));
  180. % Specify Receive structure arrays -
  181. % Define enough Receives to handle the maxPRI case. For lower PRIs, some of the Receives will go
  182. % unused in the Event list.
  183. % endDepth - add additional acquisition depth to account for some channels
  184. % having longer path lengths.
  185. maxAcqLength = ceil(sqrt(P(1).endDepth^2 + ((Trans.numelements-1)*Trans.spacing)^2));
  186. Receive = repmat(struct('Apod', zeros(1,Trans.numelements), ...
  187. 'startDepth', P(1).startDepth, ...
  188. 'endDepth', maxAcqLength, ...
  189. 'TGC', 1, ...
  190. 'bufnum', 1, ...
  191. 'framenum', 1, ...
  192. 'acqNum', 1, ...
  193. 'sampleMode', 'BS100BW',...
  194. 'mode', 0, ...
  195. 'callMediaFunc', 0),1,maxPRIs*nfrms);
  197. % - Set event specific Receive attributes.
  198. for i = 1:nfrms
  199. k = maxPRIs*(i-1);
  200. for j = 1:2:maxPRIs
  201. % -- 2D acquisition.
  202. Receive(k+j).Apod(1:128) = 1.0;
  203. Receive(k+j).framenum = i;
  204. Receive(k+j).acqNum = j;
  205. if j==1, Receive(k+j).callMediaFunc = 1; end
  206. % -- Doppler.
  207. Receive(k+j+1).Apod(33:96) = 1.0; % start Dop aperture at element 33
  208. Receive(k+j+1).TGC = 2;
  209. Receive(k+j+1).framenum = i;
  210. Receive(k+j+1).acqNum = j+1;
  211. end
  212. end
  214. % Specify Recon structure arrays.
  215. % - We need a Recon structure for 2D and one for Doppler. The 2D frame will only use
  216. % the first two 2D acquisitions of the acquisition 'frame'.
  217. % - We only need one Recon structure for the Doppler line. The Doppler reconstruction will use
  218. % nPRIs/2 acquisitions from each 'frame' for reconstruction, with each Doppler PRI reconstructed
  219. % to a different page of the IQData buffer.
  220. Recon = repmat(struct('senscutoff', 0.6, ...
  221. 'pdatanum', 1, ...
  222. 'rcvBufFrame', -1, ... % use the most recent frame
  223. 'IntBufDest', [1,1], ...
  224. 'ImgBufDest', [1,-1], ...
  225. 'RINums', zeros(1,1)), 1, 2);
  226. % - Set Recon values for 2D frame.
  227. Recon(1).RINums(1,1:2) = (1:2); % 2 ReconInfos needed for 2-1 synthetic aperture
  228. k = 3;
  229. % - Set Recon values for first Doppler ensemble.
  230. Recon(2).pdatanum = 2;
  231. Recon(2).IntBufDest = [2,1];
  232. Recon(2).ImgBufDest = [];
  233. Recon(2).RINums(1,1:(nPRIs/2)) = (k:(k+(nPRIs/2)-1)); % nPRIs/2 ReconInfos needed for Doppler.
  234. Recon(2).senscutoff = 0.8; %reduce aperture to reduce angle spread
  235. % Define ReconInfo structures.
  236. % - For 2D, we need 2 ReconInfo structures.
  237. % - For Doppler, we only need nPRIs/2 ReconInfo structures for the default case, but we will
  238. % define maxPRIs/2 structures to allow handling the maxPRI case.
  239. ReconInfo = repmat(struct('mode', 'replaceIQ', ... % set replace IQ data as default.
  240. 'txnum', 1, ...
  241. 'rcvnum', 1, ...
  242. 'pagenum',1, ...
  243. 'regionnum', 1), 1, 2 + nPRIs/2);
  244. % - Set specific ReconInfo attributes.
  245. % - ReconInfos for 2D frame.
  246. ReconInfo(1).mode = 'replaceIQ'; % replace IQ data
  247. ReconInfo(1).txnum = 1;
  248. ReconInfo(1).rcvnum = 1;
  249. ReconInfo(2).mode = 'accumIQ_replaceIntensity'; % accum and detect
  250. ReconInfo(2).txnum = 1;
  251. ReconInfo(2).rcvnum = 3;
  252. k = 2;
  253. % - ReconInfos for Doppler ensemble.
  254. for j = 1:nPRIs/2
  255. ReconInfo(k+j).mode = 'replaceIQ';
  256. ReconInfo(k+j).txnum = 2;
  257. ReconInfo(k+j).rcvnum = 2*(j-1) + 2;
  258. ReconInfo(k+j).pagenum = j;
  259. ReconInfo(k+j).regionnum = 1; % only 1 col..
  260. end
  263. % Specify Process structure arrays.
  264. pers = 20;
  265. Process(1).classname = 'Image';
  266. Process(1).method = 'imageDisplay';
  267. Process(1).Parameters = {'imgbufnum',1,... % number of buffer to process.
  268. 'framenum',-1,... % (-1 => lastFrame)
  269. 'pdatanum',1,... % number of PData structure to use
  270. 'pgain',1.0,... % pgain is image processing gain
  271. 'reject',2,... % reject level
  272. 'persistMethod','simple',...
  273. 'persistLevel',pers,...
  274. 'interpMethod','4pt',...
  275. 'grainRemoval','none',...
  276. 'processMethod','none',...
  277. 'averageMethod','none',...
  278. 'compressMethod','power',...
  279. 'compressFactor',40,...
  280. 'mappingMethod','full',...
  281. 'display',1,... % display image after processing
  282. 'displayWindow',1};
  284. Process(2).classname = 'External';
  285. Process(2).method = 'spectralDoppler';
  286. Process(2).Parameters = {'srcbuffer','inter',... % name of buffer to process.
  287. 'srcbufnum',2,...
  288. 'srcframenum',1,...
  289. 'dstbuffer','none'};
  291. % EF2 is external function for ROI plot
  292. Process(3).classname = 'External';
  293. Process(3).method = 'ROIplot';
  294. Process(3).Parameters = {'srcbuffer','none'};
  296. % Specify SeqControl structure arrays. Missing fields are set to NULL.
  297. % - Jump back to start of acquisition.
  298. SeqControl(1).command = 'jump';
  299. SeqControl(1).argument = []; % will be modified later
  300. SeqControl(2).command = 'timeToNextAcq';
  301. SeqControl(2).argument = ttna_microsec ; % time in usec
  302. % loopCnt/loopTst are used to implement a conditional jump
  303. SeqControl(3).command = 'loopCnt'; % for 2D only
  304. SeqControl(3).argument = 0;
  305. SeqControl(4).command = 'loopCnt'; % for doppler
  306. SeqControl(4).argument = 1;
  308. nsc = 5; % nsc is count for next SeqControl object
  310. n = 1; % n is count for next Event
  312. Event(n).info = 'ROI plot';
  313. Event(n).tx = 0;
  314. Event(n).rcv = 0;
  315. Event(n).recon = 0;
  316. Event(n).process = 3;
  317. Event(n).seqControl = 0;
  318. n = n+1;
  320. Event(n).info = 'Start here for 2D only processing.';
  321. Event(n).tx = 0;
  322. Event(n).rcv = 0;
  323. Event(n).recon = 0;
  324. Event(n).process = 0;
  325. Event(n).seqControl = 3;
  326. n = n+1;
  328. Event(n).info = 'Jump to start of acquisitions';
  329. Event(n).tx = 0;
  330. Event(n).rcv = 0;
  331. Event(n).recon = 0;
  332. Event(n).process = 0;
  333. Event(n).seqControl = 1;
  334. n = n+1;
  336. Event(n).info = 'Start here for Doppler only processing.';
  337. Event(n).tx = 0;
  338. Event(n).rcv = 0;
  339. Event(n).recon = 0;
  340. Event(n).process = 0;
  341. Event(n).seqControl = 4;
  342. n = n+1;
  344. nStartAcq = n;
  345. SeqControl(1).argument = nStartAcq;
  347. for i = 1:nfrms % Acquire frames
  348. k = maxPRIs*(i-1);
  349. for j = 1:2:nPRIs % acquisition repeats every 2 acquisitions
  350. Event(n).info = '2D acquisition.';
  351. Event(n).tx = 1;
  352. Event(n).rcv = k+j;
  353. Event(n).recon = 0;
  354. Event(n).process = 0;
  355. Event(n).seqControl = 2;
  356. n = n+1;
  358. Event(n).info = 'Doppler acquisition.';
  359. Event(n).tx = 2;
  360. Event(n).rcv = k+j+1;
  361. Event(n).recon = 0;
  362. Event(n).process = 0;
  363. Event(n).seqControl = 2;
  364. n = n+1;
  365. end
  367. Event(n).info = 'transfer acquired frame data to host';
  368. Event(n).tx = 0;
  369. Event(n).rcv = 0;
  370. Event(n).recon = 0;
  371. Event(n).process = 0;
  372. Event(n).seqControl = nsc;
  373. SeqControl(nsc).command = 'transferToHost';
  374. nsc = nsc+1;
  375. n = n+1;
  377. Event(n).info = 'test loopCnt';
  378. Event(n).tx = 0;
  379. Event(n).rcv = 0;
  380. Event(n).recon = 0;
  381. Event(n).process = 0;
  382. Event(n).seqControl = nsc;
  383. SeqControl(nsc).command = 'loopTst';
  384. SeqControl(nsc).argument = n+3; % jump to Doppler if nz
  385. nsc = nsc+1;
  386. n = n+1;
  388. Event(n).info = 'recon and process 2D';
  389. Event(n).tx = 0;
  390. Event(n).rcv = 0;
  391. Event(n).recon = 1;
  392. Event(n).process = 1;
  393. Event(n).seqControl = 0;
  394. n = n+1;
  396. Event(n).info = 'jump over Doppler';
  397. Event(n).tx = 0;
  398. Event(n).rcv = 0;
  399. Event(n).recon = 0;
  400. Event(n).process = 0;
  401. Event(n).seqControl = nsc;
  402. SeqControl(nsc).command = 'jump';
  403. SeqControl(nsc).argument = n+3;
  404. nsc = nsc+1;
  405. n = n+1;
  407. Event(n).info = 'recon and process Doppler';
  408. Event(n).tx = 0;
  409. Event(n).rcv = 0;
  410. Event(n).recon = 2;
  411. Event(n).process = 2;
  412. Event(n).seqControl = 0;
  413. n = n+1;
  415. Event(n).info = 'set loopCnt back to 1';
  416. Event(n).tx = 0;
  417. Event(n).rcv = 0;
  418. Event(n).recon = 0;
  419. Event(n).process = 0;
  420. Event(n).seqControl = 4;
  421. n = n+1;
  423. Event(n).info = 'exit to Matlab';
  424. Event(n).tx = 0;
  425. Event(n).rcv = 0;
  426. Event(n).recon = 0;
  427. Event(n).process = 0;
  428. Event(n).seqControl = 0;
  429. % Exit to Matlab every 3rd frame
  430. if floor(i/3) == i/3
  431. Event(n).seqControl = nsc;
  432. SeqControl(nsc).command = 'returnToMatlab';
  433. nsc = nsc+1;
  434. end
  435. n = n+1;
  436. end
  438. Event(n).info = 'Jump back to the start of aquisition';
  439. Event(n).tx = 0;
  440. Event(n).rcv = 0;
  441. Event(n).recon = 0;
  442. Event(n).process = 0;
  443. Event(n).seqControl = 1;
  446. % User specified UI Control Elements
  447. import vsv.seq.uicontrol.VsSliderControl;
  449. % - Sensitivity Cutoff
  450. UI(1).Control = VsSliderControl( 'LocationCode', 'UserB7', ...
  451. 'Label', 'Sens. Cutoff', ...
  452. 'SliderMinMaxVal', [ 0,1.0,Recon(1).senscutoff], ...
  453. 'SliderStep', [0.025,0.1], ...
  454. 'ValueFormat', '%1.3f', ...
  455. 'Callback', @sensitivityCutoffCallback );
  458. % - Range Change
  459. MinMaxVal = [64,300,P(1).endDepth ]; % default unit is wavelength
  460. AxesUnit = 'wls';
  461. if isfield(Resource.DisplayWindow(1),'AxesUnits')&&~isempty(Resource.DisplayWindow(1).AxesUnits)
  462. if strcmp(Resource.DisplayWindow(1).AxesUnits,'mm')
  463. AxesUnit = 'mm';
  464. MinMaxVal = MinMaxVal * (Resource.Parameters.speedOfSound/1000/Trans.frequency);
  465. end
  466. end
  467. UI(2).Control = VsSliderControl( 'LocationCode', 'UserA1','Label',['Range (',AxesUnit,')'],...
  468. 'SliderMinMaxVal',MinMaxVal,'SliderStep',[0.1,0.2],'ValueFormat','%3.0f', ...
  469. 'Callback', @rangeChangeCallback);
  471. % - PRF control
  472. UI(3).Control = VsSliderControl( 'LocationCode', 'UserB4','Label','Doppler PRF',...
  473. 'SliderMinMaxVal',[minDopPRF,maxDopPRF,dopPRF],...
  474. 'SliderStep',[100/ (maxDopPRF-minDopPRF),200/ (maxDopPRF-minDopPRF)],'ValueFormat','%4.0f Hz', ...
  475. 'Callback', @dopplerPRFCallback);
  477. % - Wall Filter control
  478. UI(4).Control = VsSliderControl( 'LocationCode','UserB3','Label','Doppler WF',...
  479. 'SliderMinMaxVal',[8,0.1*maxDopPRF,dopWFCutoffNorm*dopPRF],...
  480. 'SliderStep',[0.02,0.2],'ValueFormat','%4.0f Hz', ...
  481. 'Callback', @dopplerWallFilterCallback);
  483. % - Sweep Time control
  484. UI(5).Control = VsSliderControl('LocationCode', 'UserB2','Label','Sweep Time',...
  485. 'SliderMinMaxVal',[min(sgp.THistAllow),max(sgp.THistAllow),sweepTime],...
  486. 'SliderStep',[0.25,0.25],'ValueFormat','%1.0f s', ...
  487. 'Callback', @sweepTimeCallback);
  489. % - Baseline control
  490. UI(6).Control = VsSliderControl('LocationCode', 'UserB1','Label','Baseline',...
  491. 'SliderMinMaxVal',[-0.5,0.5,baseLineShiftNorm],...
  492. 'SliderStep',[0.05,0.1],'ValueFormat','%1.2f', ...
  493. 'Callback', @baselineCallback );
  495. % - Window ButtonDown callback for setting sample volume position.
  496. UI(7).Callback = @wbdCallback;
  497. UI(7).Statement = @()setCallback(Resource.DisplayWindow(1).Type);
  499. % external functions
  500. import vsv.seq.function.ExFunctionDef;
  501. EF(1).Function = ExFunctionDef('setCallback', @setCallback);
  502. EF(2).Function = ExFunctionDef('ROIplot', @ROIplot );
  505. % Specify factor for converting sequenceRate to frameRate.
  506. frameRateFactor = 3;
  508. % Save all the structures to a .mat file.
  509. filename = 'MatFiles/L11-5vSpectralDoppler';
  511. % Save all the structures to a .mat file.
  512. save(filename);
  514. %% **** Callback routines used by External function definition (EF) ****
  515. function sensitivityCutoffCallback(~, ~, UIValue)
  517. ReconL = evalin('base', 'Recon');
  518. for i = 1:size(ReconL,2)
  519. ReconL(i).senscutoff = UIValue;
  520. end
  521. assignin('base','Recon',ReconL);
  522. Control = evalin('base','Control');
  523. Control.Command = 'update&Run';
  524. Control.Parameters = {'Recon'};
  525. assignin('base','Control', Control);
  526. return
  527. end
  529. function rangeChangeCallback(hObject, ~, UIValue )
  530. simMode = evalin('base','Resource.Parameters.simulateMode');
  531. % No range change if in simulate mode 2.
  532. if simMode == 2
  533. set(hObject,'Value',evalin('base','P.endDepth'));
  534. return
  535. end
  536. Trans = evalin('base','Trans');
  537. Resource = evalin('base','Resource');
  538. scaleToWvl = Trans.frequency/(Resource.Parameters.speedOfSound/1000);
  540. P = evalin('base','P');
  541. P(1).endDepth = UIValue;
  542. if isfield(Resource.DisplayWindow(1),'AxesUnits')&&~isempty(Resource.DisplayWindow(1).AxesUnits)
  543. if strcmp(Resource.DisplayWindow(1).AxesUnits,'mm')
  544. P(1).endDepth = UIValue*scaleToWvl;
  545. end
  546. end
  547. assignin('base','P',P);
  549. evalin('base','PData(1).Size(1) = ceil((P(1).endDepth-P(1).startDepth)/PData(1).PDelta(3));');
  550. evalin('base','PData(1).Region = computeRegions(PData(1));');
  551. evalin('base','Resource.DisplayWindow(1).Position(4) = ceil(PData(1).Size(1)*PData(1).PDelta(3)/Resource.DisplayWindow(1).pdelta);');
  552. Receive = evalin('base', 'Receive');
  554. maxAcqLength = ceil(sqrt(P(1).endDepth^2 + ((Trans.numelements-1)*Trans.spacing)^2));
  555. for i = 1:size(Receive,2)
  556. Receive(i).endDepth = maxAcqLength;
  557. end
  558. assignin('base','Receive',Receive);
  559. evalin('base','TGC(1).rangeMax = P(1).endDepth;');
  560. evalin('base','TGC(1).Waveform = computeTGCWaveform(TGC(1));');
  562. Control = evalin('base','Control');
  563. Control.Command = 'update&Run';
  564. Control.Parameters = {'PData','InterBuffer','ImageBuffer','Receive','TGC','Recon','DisplayWindow'};
  565. assignin('base','Control', Control);
  566. assignin('base', 'action', 'displayChange');
  567. return
  568. end
  570. function dopplerPRFCallback( hObject, ~, UIValue)
  572. dopPRFnom = UIValue;
  573. framePeriod = evalin('base','framePeriod');
  574. psched = spectralDoppler('restrictAcqPRF',round(framePeriod*1e6),dopPRFnom);
  575. acqPRF = psched.PRFAcq ;
  576. dopPRF = psched.PRFDop ;
  577. ttna_microsec = psched.PRIAcq_uSec ;
  578. % ttnaNom_microsec = psched.PRIAcq_uSec ;
  579. framePeriod = psched.FrameTime_uSec*1e-6 ;
  580. nPRIs= psched.pulsesPerFrameAcq ;
  581. nDopPRIs = psched.pulsesPerFrameDop ;
  582. % maxPRIs = psched.pulsesPerFrameAcqMax ;
  584. set(hObject,'Value',dopPRF);
  585. assignin('base', 'dopPRF', dopPRF);
  586. assignin('base', 'acqPRF', acqPRF);
  587. assignin('base', 'framePeriod', framePeriod);
  589. nfrms = evalin('base','nfrms');
  590. maxPRIs = evalin('base','maxPRIs');
  591. assignin('base','nDopPRIs',nDopPRIs);
  592. assignin('base','nPRIs',nPRIs);
  593. % Update the Doppler Recon to specify nDopPRIs ReconInfo structures.
  594. Recon = evalin('base','Recon');
  595. Recon(2).RINums(1,1:nDopPRIs) = (3:(3+(nDopPRIs)-1));
  596. assignin('base', 'Recon', Recon);
  598. ReconInfo = evalin('base','ReconInfo');
  599. % - ReconInfos for Doppler ensemble.
  600. k = 2;
  601. for j = 1:nPRIs/2
  602. ReconInfo(k+j).mode = 'replaceIQ';
  603. ReconInfo(k+j).txnum = 2;
  604. ReconInfo(k+j).rcvnum = 2*(j-1) + 2;
  605. ReconInfo(k+j).pagenum = j;
  606. ReconInfo(k+j).regionnum = 1; % only 1 col..
  607. end
  608. assignin('base','ReconInfo',ReconInfo);
  610. % Re-compute Event structures.
  611. Event = evalin('base','Event');
  612. nStartAcq = evalin('base','nStartAcq');
  613. n = nStartAcq;
  614. Event = Event(1:n-1); % throw out all but preamble
  615. SeqControl = evalin('base','SeqControl');
  616. nsc =5;
  617. SeqControl = SeqControl(1:nsc-1); % throw out all but those prior to nsc
  618. SeqControl(2).argument = ttna_microsec;
  619. % Re-build the Event list.
  620. for i = 1:nfrms % Acquire frames
  621. k = maxPRIs*(i-1);
  622. for j = 1:2:nPRIs % acquisition repeats every 2 acquisitions
  623. Event(n)=struct('info','2D acquisition.',...
  624. 'tx',1,'rcv',k+j,'recon',0,'process',0,'seqControl',2);
  625. n = n+1;
  626. Event(n)=struct('info','Doppler acquisition.',...
  627. 'tx',2,'rcv',k+j+1,'recon',0,'process',0,'seqControl',2);
  628. n = n+1;
  629. end
  630. Event(n)=struct('info','transfer acquired frame data to host',...
  631. 'tx',0,'rcv',0,'recon',0,'process',0,'seqControl',nsc);
  632. SeqControl(nsc).command = 'transferToHost';
  633. nsc = nsc+1;
  634. n = n+1;
  635. Event(n)=struct('info','test loopCnt',...
  636. 'tx',0,'rcv',0,'recon',0,'process',0,'seqControl',nsc);
  637. SeqControl(nsc).command = 'loopTst';
  638. SeqControl(nsc).argument = n+3; % jump to Doppler if nz
  639. nsc = nsc+1;
  640. n = n+1;
  641. Event(n)=struct('info','recon and process 2D',...
  642. 'tx',0,'rcv',0,'recon',1,'process',1,'seqControl',0);
  643. n = n+1;
  644. Event(n)=struct('info','jump over Doppler',...
  645. 'tx',0,'rcv',0,'recon',0,'process',0,'seqControl',nsc);
  646. SeqControl(nsc).command = 'jump';
  647. SeqControl(nsc).argument = n+3;
  648. nsc = nsc+1;
  649. n = n+1;
  650. Event(n)=struct('info','recon and process Doppler',...
  651. 'tx',0,'rcv',0,'recon',2,'process',2,'seqControl',0);
  652. n = n+1;
  653. Event(n)=struct('info','set loopCnt back to 1',...
  654. 'tx',0,'rcv',0,'recon',0,'process',0,'seqControl',4);
  655. n = n+1;
  656. Event(n)=struct('info','exit to Matlab',...
  657. 'tx',0,'rcv',0,'recon',0,'process',0,'seqControl',0);
  658. % Exit to Matlab every 3rd frame
  659. if floor(i/3) == i/3
  660. Event(n).seqControl = nsc;
  661. SeqControl(nsc).command = 'returnToMatlab';
  662. nsc = nsc+1;
  663. end
  664. n = n+1;
  665. end
  666. Event(n)=struct('info','Jump back to first event',...
  667. 'tx',0,'rcv',0,'recon',0,'process',0,'seqControl',1);
  669. assignin('base', 'Event', Event);
  670. assignin('base', 'SeqControl', SeqControl);
  671. % Update VDAS parameters for Receive objects
  672. evalin('base','VsUpdate(''Receive'')');
  673. % Set Control.Command to update changed structures in runAcq.
  674. Control = evalin('base','Control');
  675. Control.Command = 'update&Run';
  676. Control.Parameters = {'Recon','Event','SeqControl'};
  677. assignin('base','Control', Control);
  678. % Update the WF control:
  679. hwf = findobj('tag','UserB3Slider');
  680. dopWFCutoffNorm = evalin('base' ,'dopWFCutoffNorm');
  681. set(hwf,'Value',dopPRF*dopWFCutoffNorm);
  682. hwf = findobj('tag','UserB3Edit');
  683. set(hwf,'String',num2str(dopPRF*dopWFCutoffNorm,'%4.0f Hz'));
  684. return
  685. end
  687. function dopplerWallFilterCallback(~, ~, UIValue)
  689. dopPRF = evalin('base','dopPRF');
  690. dopWFCutoffNorm = UIValue/dopPRF;
  691. assignin('base', 'dopWFCutoffNorm', dopWFCutoffNorm);
  692. return
  694. end
  696. function sweepTimeCallback( hObject, ~, UIValue)
  697. %-UI#5Callback - Sweep Time
  698. sweepTime = round(UIValue);
  699. TFrame=evalin('base','framePeriod');
  700. sgp=spectralDoppler('spectrogramParameters',TFrame,1);
  701. [~,swInd] = min(abs(sgp.THistAllow-sweepTime));
  702. %sweepTimeAllowed = sgp.THistAllow(swInd);
  704. dopSweepTimeIndex = swInd;
  706. assignin('base', 'dopSweepTimeIndex', dopSweepTimeIndex);
  707. set(hObject,'Value',sweepTime);
  708. assignin('base', 'sweepTime', sweepTime);
  709. return
  710. end
  713. function baselineCallback( hObject, ~, UIValue)
  714. %-UI#6Callback - Baseline
  715. baseLineShiftNorm = UIValue;
  716. baseLineShiftNorm = round(baseLineShiftNorm*20)/20;
  717. set(hObject,'Value',baseLineShiftNorm);
  718. assignin('base', 'baseLineShiftNorm', baseLineShiftNorm);
  719. return
  720. end
  722. function wbdCallback(varargin)
  723. % Window ButtonDown callback for sample volume positioning.
  724. persistent init wbFig wbAxes elypHndl
  725. Trans = evalin('base','Trans');
  726. Resource = evalin('base','Resource');
  727. DopRegionLim = evalin('base','DopRegionLim');
  729. if isempty(init)
  730. init = 1;
  731. elypHndl = 0;
  732. end
  734. % Get pos ofmouse click and ensure the unit is wavelength for spectral doppler
  735. VsType = Resource.DisplayWindow(1).Type;
  736. if strcmp(VsType,'Matlab')
  737. hObject = varargin{1};
  738. wbFig = evalin('base','Resource.DisplayWindow(1).figureHandle');
  739. wbAxes = get(wbFig,'CurrentAxes');
  740. cp = get(wbAxes,'CurrentPoint');
  741. if isfield(Resource.DisplayWindow(1),'AxesUnits')&&~isempty(Resource.DisplayWindow(1).AxesUnits)
  742. if strcmp(Resource.DisplayWindow(1).AxesUnits,'mm')
  743. scaleToWvl = Trans.frequency/(Resource.Parameters.speedOfSound/1000);
  744. % wl2mm = (Resource.Parameters.speedOfSound/1000)/Trans.frequency;
  745. cp = cp*scaleToWvl;
  746. unitMm = 1;
  747. end
  748. else
  749. unitMm = 0;
  750. end
  751. % Check for sample volume outside of measurement region.
  752. x = min(max(cp(1,1),DopRegionLim.x(1)),DopRegionLim.x(2));
  753. z = min(max(cp(1,2),DopRegionLim.y(1)),DopRegionLim.y(2));
  754. else
  755. mct = evalin('base','mct');
  756. mouseButton = mct.buttonName;
  757. switch string(mouseButton)
  758. case 'Start'
  759. return
  760. case 'Left'
  761. hObject.SelectionType = 'normal';
  762. imageViewer = evalin('base','imageViewer');
  763. imageCanvas = imageViewer(1).getImageCanvas();
  764. srcImage = imageCanvas.getSrcImage;
  765. x = mct.xImgPos/srcImage.pixelUnitScaling;
  766. z = mct.yImgPos/srcImage.pixelUnitScaling;
  767. case 'Right'
  768. hObject.SelectionType = 'alt';
  769. end
  770. end
  772. % Change Event Sequence if left mouse button is pressed
  773. if strcmp(hObject.SelectionType,'normal')
  774. if elypHndl == 0
  775. % set startEvent for Doppler only.
  776. Control = evalin('base','Control');
  777. Control(2).Command = 'set&Run';
  778. Control(2).Parameters = {'Parameters',1,'startEvent',4};
  779. evalin('base','Resource.Parameters.startEvent = 4;');
  780. else
  781. delete(elypHndl); % delete previous annotation circle
  782. end
  784. if strcmp(VsType,'Matlab')
  785. % set annotation in the Matlab Viewer (Verasonics Viewer is done in MouseClickTool)
  786. abox = [x-1,z-1,2,2];
  787. axun = get(wbAxes,'Units'); % save axis units
  788. set(wbAxes,'Units','normalized'); % make axes units normalized
  789. axpos = get(wbAxes,'Position'); % get axes position
  790. axlim = axis(wbAxes); % get the axis limits [xlim ylim (zlim)]
  791. if unitMm, axlim = axlim*scaleToWvl; end
  792. axwidth = diff(axlim(1:2));
  793. axheight = diff(axlim(3:4));
  794. % Transform from data space coordinates to normalized figure coordinates
  795. bbox(1) = (abox(1)-axlim(1))/axwidth * axpos(3) + axpos(1);
  796. bbox(2) = (axlim(4)-abox(2))/axheight * axpos(4) + axpos(2);
  797. bbox(3) = abox(3) * axpos(3)/axwidth;
  798. bbox(4) = abox(4) * axpos(4)/axheight;
  799. set(wbAxes,'Units',axun); % restore axis units
  800. elypHndl = annotation('ellipse',bbox,'EdgeColor',[1 .2 .2],'LineWidth',1.0);
  801. end
  803. assignin('base','SVPos',[x,z-2])
  804. %Modify structures for new SV position.
  805. evalin('base','PData(2).Origin = [SVPos(1),0,SVPos(2)];');
  806. evalin('base','PData(2).Region=computeRegions(PData(2));');
  808. Control(1).Command = 'update&Run';
  809. Control(1).Parameters = {'PData'};
  810. assignin('base','Control', Control);
  811. % if right mouse button ...
  812. elseif strcmp(hObject.SelectionType,'alt')
  813. % delete annotation circle
  814. if elypHndl ~= 0
  815. delete(elypHndl);
  816. elypHndl = 0;
  817. end
  818. % set startEvent for 2D only
  819. Control.Command = 'set&Run';
  820. Control.Parameters = {'Parameters',1,'startEvent',1};
  821. evalin('base','Resource.Parameters.startEvent = 1;');
  822. assignin('base','Control',Control);
  823. end
  824. return
  826. end
  828. %% **** Callback routines used by External function definition (EF) ****
  830. function setCallback(VsType)
  831. switch VsType
  832. case 'Verasonics'
  834. vantageWindow = evalin('base','vantageWindow');
  835. imageViewer = evalin('base','imageViewer');
  836. DopRegionLim = evalin('base','DopRegionLim');
  837. mct = javaObjectEDT( 'com.verasonics.viewer.tools.mouseclicktool.MouseClickTool', vantageWindow, imageViewer(1));
  838. mcth = javaObjectEDT( handle(mct, 'callbackproperties' ) );
  839. mct.setToolEnabled(true);
  840. mct.lowerLimitX = DopRegionLim.x(1);
  841. mct.upperLimitX = DopRegionLim.x(2);
  842. mct.lowerLimitY = DopRegionLim.y(1);
  843. mct.upperLimitY = DopRegionLim.y(2);
  844. mcth.ClickedEventCallback = @wbdCallback;
  845. assignin('base','mct',mct);
  846. case 'Matlab'
  847. evalin('base','set(Resource.DisplayWindow(1).figureHandle,''WindowButtonDownFcn'',@wbdCallback);');
  848. end
  849. return
  850. end
  852. function ROIplot(varargin)
  853. %ROIplot
  854. persistent drawROI
  856. % drawRegionOutline(WinNum,PDataNum,RegionNum) creates an outline from
  857. % PData(PDataNum).Region(RegionNum) on displayWindow(WinNum) with default color - white.
  858. if isempty(drawROI)
  859. drawROI = 1;
  860. evalin('base','hROI = drawRegionOutline(1,3,1);')
  861. else
  862. evalin('base','drawRegionOutline(hROI,1,3,1);')
  863. end
  865. return
  866. end

SetUpL11_5vSpectralDoppler.m, no license · at the source

Overview

Authors: Max J Kerensky1,2, Siddharth Krishnan2,3, Ruixing Liang2,4, Kelley M Kempski Leadingham2,3, Victor M Quiroz1,5, Joshua Punnoose2,3, Constantin Smit2,3, Denis Routkevitch1,2,3, Avisha Kumar2,4, A Daniel Davidar2,3, Leonard Steger2,3, Carly Weber-Levine2,3, Kelly Jiang2,3, Meghana Bhimreddy2,3, Stuart J Bauer1,5, Angelica F Lopez1,2, Patrick Kramer2,3, Kayla Robinson2,6, Arjun K Menta2,3, Abdul Karim Ghaith2,3
and 22 other authorsAndrew M Hersh2,3, Haley G Abramson1,2,7, Ali Mohammadabadi2,3, John N Theodore1,5, Osamah M Zmily1,5, Ritvik Jillala2,3, Vikas Vattipally2,3, David Kopala1,2, Siavash S Barough8, Mohammad Hossein Amini9, Jonathan Maltz10, Francisco Chavez11, Kyle Morrison11, Laura Roy12, Ian Suk3, Ryan P Lee3, Betty Tyler3, Mark Luciano3, Nitish V Thakor1,2,4, Joshua C Doloff1,5,13, Nicholas Theodore1,2,3,14,15, Amir Manbachi1,2,3,4,6,16
16 affiliations
  1. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
  2. HEPIUS Innovation Laboratory, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
  3. Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
  4. Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, USA
  5. Translational Therapeutics & Regenerative Engineering Center, Johns Hopkins University, Baltimore, MD, USA
  6. Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
  7. Advanced Patient Monitoring, Becton, Dickinson, and Company, Irvine, CA, USA
  8. Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
  9. Fujifilm Visualsonics Inc., Toronto, ON, Canada
  10. Molecular Biophysics and Integrated Bioimaging, Berkeley Lab, University of California, Berkeley, CA, USA
  11. Sonic Concepts Inc., Bothell, WA, USA
  12. Roy Illustration, New York, NY, USA
  13. Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
  14. Department of Orthopaedic Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
  15. Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
  16. Department of Anesthesiology and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
Journal: Science advances, volume 12, issue 45, article eaeg2342
Dates: received 8 February 2026; accepted 1 October 2026; published online 4 November 2026; in print November 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI · PMCID PMC13733905
Status: code verified (how the code is found and verified)
Categories: other (modality), clinical / translational (subfield)
Methods: Spectral & time-frequency, fMRI & imaging, Physiology & signal measures
Citations: not cited yet (Europe PMC); 91 references in the paper

Abstract

The days following decompression surgery for acute spinal cord injury (SCI) are a critical period for postoperative monitoring. After wound closure, clinicians lack on-demand access to local spinal cord morphology and hemodynamics, and care therefore remains guided largely by systemic surrogates rather than direct postoperative insight into the injured cord. We present the Multimodal Ultrasound System for Injury Care (MUSIC), a temporary epidural ultrasound neural interface placed during standard decompression surgery to enable postoperative brightness-mode imaging, Doppler-derived hemodynamic monitoring, and future device-integrated ultrasound actuation. Across simulations, benchtop, human cadaveric, and porcine studies, MUSIC enabled on-demand visualization of cord structure, hematoma tracking, detection and longitudinal tracking of localized Doppler flow signatures attributable to the sulcal artery region, and, in healthy pigs, proof-of-concept focused ultrasound modulation of blood-flow velocity. MUSIC establishes a temporary postoperative acoustic interface that provides spinal cord information to inform monitoring, future management, and localized intervention strategies after SCI.

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

Zenodo 22908234

License: none: the authors keep all their rights
State: the link answers, verified on 7 November 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data, code, and materials availability:”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Signal Processing Toolbox (7 files), Image Processing Toolbox (6 files), Statistics and Machine Learning Toolbox (5 files), Wavelet Toolbox (4 files), SciPy (3 files)
Availability: 1 check, the latest on 7 November 2026: the link answers (HTTP 200)
  • 7 November 2026: the link answers (HTTP 200)
267 files
At the source: doi.org/10.5281/zenodo.22908234

Zenodo 22907737

License: Apache-2.0
State: the link answers, verified on 7 November 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data, code, and materials availability:”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Matplotlib (5 files), NumPy (5 files), pandas (4 files), SciPy (4 files), seaborn (3 files), scikit-learn (2 files), Plotly (1 file), statannotations (1 file), statsmodels (1 file)
Availability: 1 check, the latest on 7 November 2026: the link answers (HTTP 200)
  • 7 November 2026: the link answers (HTTP 200)
8 files
At the source: doi.org/10.5281/zenodo.22907737

Zenodo 22908477

License: none: the authors keep all their rights
State: the link answers, verified on 7 November 2026
Evidence: files inventoried
Size: 1 file
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 7 November 2026: the link answers (HTTP 200)
  • 7 November 2026: the link answers (HTTP 200)
7 files
At the source: doi.org/10.5281/zenodo.22908477

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;
  • 282 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 and the permanent repositories cited here. Experimental data and analyses are archived in Dryad at https://doi.org/10.5061/dryad.nk98sf891. Publication-version software associated with MUSIC imaging, focused-ultrasound analysis, and the MUSIC mobile application is archived in Zenodo at https://doi.org/10.5281/zenodo.22908234, https://doi.org/10.5281/zenodo.22907737, and https://doi.org/10.5281/zenodo.22908477, respectively. The corresponding development repositories are available through the HEPIUS Lab GitHub organization at https://github.com/HEPIUSLAB. This study did not generate new materials.

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

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Version 1, 7 November 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 42 authors, 74 references.

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This paper

Kerensky, M. J., Krishnan, S., Liang, R., Kempski Leadingham, K. M., Quiroz, V. M., Punnoose, J., Smit, C., Routkevitch, D., Kumar, A., Davidar, A. D., Steger, L., Weber-Levine, C., Jiang, K., Bhimreddy, M., Bauer, S. J., Lopez, A. F., Kramer, P., Robinson, K., Menta, A. K., . . . Manbachi, A. (2026). Ultrasound neural interface enabling acute spinal cord monitoring and blood flow modulation. Science advances, 12(45), eaeg2342.

BibTeX

@article{kerensky2026ultrasound,
author = {Kerensky, Max J and Krishnan, Siddharth and Liang, Ruixing and Kempski Leadingham, Kelley M and Quiroz, Victor M and Punnoose, Joshua and Smit, Constantin and Routkevitch, Denis and Kumar, Avisha and Davidar, A Daniel and Steger, Leonard and Weber-Levine, Carly and Jiang, Kelly and Bhimreddy, Meghana and Bauer, Stuart J and Lopez, Angelica F and Kramer, Patrick and Robinson, Kayla and Menta, Arjun K and Ghaith, Abdul Karim and Hersh, Andrew M and Abramson, Haley G and Mohammadabadi, Ali and Theodore, John N and Zmily, Osamah M and Jillala, Ritvik and Vattipally, Vikas and Kopala, David and Barough, Siavash S and Amini, Mohammad Hossein and Maltz, Jonathan and Chavez, Francisco and Morrison, Kyle and Roy, Laura and Suk, Ian and Lee, Ryan P and Tyler, Betty and Luciano, Mark and Thakor, Nitish V and Doloff, Joshua C and Theodore, Nicholas and Manbachi, Amir},
title = {{Ultrasound neural interface enabling acute spinal cord monitoring and blood flow modulation}},
journal = {Science advances},
year = {2026},
month = nov,
volume = {12},
number = {45},
pages = {eaeg2342},
publisher = {American Association for the Advancement of Science},
issn = {2375-2548},
pmcid = {PMC13733905}
}

RIS

TY - JOUR
AU - Kerensky, Max J
AU - Krishnan, Siddharth
AU - Liang, Ruixing
AU - Kempski Leadingham, Kelley M
AU - Quiroz, Victor M
AU - Punnoose, Joshua
AU - Smit, Constantin
AU - Routkevitch, Denis
AU - Kumar, Avisha
AU - Davidar, A Daniel
AU - Steger, Leonard
AU - Weber-Levine, Carly
AU - Jiang, Kelly
AU - Bhimreddy, Meghana
AU - Bauer, Stuart J
AU - Lopez, Angelica F
AU - Kramer, Patrick
AU - Robinson, Kayla
AU - Menta, Arjun K
AU - Ghaith, Abdul Karim
AU - Hersh, Andrew M
AU - Abramson, Haley G
AU - Mohammadabadi, Ali
AU - Theodore, John N
AU - Zmily, Osamah M
AU - Jillala, Ritvik
AU - Vattipally, Vikas
AU - Kopala, David
AU - Barough, Siavash S
AU - Amini, Mohammad Hossein
AU - Maltz, Jonathan
AU - Chavez, Francisco
AU - Morrison, Kyle
AU - Roy, Laura
AU - Suk, Ian
AU - Lee, Ryan P
AU - Tyler, Betty
AU - Luciano, Mark
AU - Thakor, Nitish V
AU - Doloff, Joshua C
AU - Theodore, Nicholas
AU - Manbachi, Amir
TI - Ultrasound neural interface enabling acute spinal cord monitoring and blood flow modulation
T2 - Science advances
J2 - Sci Adv
PY - 2026
DA - 2026/11/06
VL - 12
IS - 45
SP - eaeg2342
SN - 2375-2548
PB - American Association for the Advancement of Science
LA - en
ER -

CSL-JSON

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{
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{
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{
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{
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{
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{
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"publisher": "American Association for the Advancement of Science",
"language": "en",
"issued": {
"date-parts": [
[
2026,
11,
6
]
]
}
}

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