http://www.k-wave.org/forum/topic/getting-started-with-mrict-scans-intracranial-pressure-maps-skull-aberration Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 23:32:16 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/getting-started-with-mrict-scans-intracranial-pressure-maps-skull-aberration#post-6368 Thu, 22 Mar 2018 19:38:45 +0000 Hammerben1 6368@http://www.k-wave.org/forum/ <p>Thank you! </p> http://www.k-wave.org/forum/topic/getting-started-with-mrict-scans-intracranial-pressure-maps-skull-aberration#post-6361 Wed, 21 Mar 2018 21:36:36 +0000 Bradley Treeby 6361@http://www.k-wave.org/forum/ <p>Hi Ben,</p> <p>It should be straightforward. First load the CT data into MATLAB using an appropriate dicom or nifty reader. Assemble the data into a 3D matrix, then pass to the function. You will need to check that the Hounsfield Units in your dataset are scaled in the same way as expected by <code>hounsfield2density</code> (see <a href="http://www.k-wave.org/forum/topic/replace-the-phantom-with-a-3d-ct-volume#post-6268">this thread</a>).</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/getting-started-with-mrict-scans-intracranial-pressure-maps-skull-aberration#post-6352 Tue, 20 Mar 2018 00:01:47 +0000 Hammerben1 6352@http://www.k-wave.org/forum/ <p>Hi Brad:<br /> This is exactly what we are trying to do as well.<br /> So basically we could use hounsfield2density to transfer a CT scan to a spatial profile of densities. Can you dig deeper into this topic? Exactly how would you do that?<br /> Is there an example for conversion CT scan to a spatial profile of skull density?<br /> Thank you so much in advance!</p> <p>Ben </p> http://www.k-wave.org/forum/topic/getting-started-with-mrict-scans-intracranial-pressure-maps-skull-aberration#post-6323 Wed, 07 Mar 2018 22:33:00 +0000 Bradley Treeby 6323@http://www.k-wave.org/forum/ <p>Hi Justin,</p> <p>You could import the skull geometry from a CT scan, and then either use <code>hounsfield2density</code>, or one of the conversion algorithms based on porosity reported in the literature, e.g., <a href="https://doi.org/10.1121/1.1529663">this paper</a>. If you use the <code>makeBowl</code> function to define your transducer, it should be straightforward to orient it in the desired direction. Regarding the wave amplitude, for neuromodulation, the wave propagation is linear, so the amplitude of the output will be proportional to the amplitude of the input. If you're trying to simulate an experimental setup, you calibrate the input amplitude using a hydrophone measurement.</p> <p>Hope that helps,</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/getting-started-with-mrict-scans-intracranial-pressure-maps-skull-aberration#post-6308 Fri, 02 Mar 2018 17:47:06 +0000 jmfine 6308@http://www.k-wave.org/forum/ <p>I have a few questions to try and get started on a (potentially lofty) goal. At the moment, we are using single element transducers to do low frequency neuromodulation. Clearly the skull causes both attenuation and distortion of ultrasound (assumption is that gray/white matter soft tissue has neglect-able impact). I am (first) trying to both estimate the intracranial pressure map and extent of skull distortion of the beam for this single transducer setup. Then, I would like to be able to do the same for a 4 element phased array that will allow beam steering etc...<br /> In this paper (<a href="http://iopscience.iop.org/article/10.1088/1741-2552/aa843e/pdf" rel="nofollow">http://iopscience.iop.org/article/10.1088/1741-2552/aa843e/pdf</a>) they did something similar for the single transducer setup. </p> <p>How would I best get started to replicate that? Is this under the<br /> Heterogeneous Propagation Medium Example"? I have gone thru the example code already and ran it successfully and altered the transducer freq, etc.. Nonetheless, I am not sure how to program in the parameters (speed of sound, density, attenuation) for all of the layers (bone, etc). Furthermore, I am unsure what the appropriate initial pressure setting should be.</p> <p>Furthermore, how would I go about defining the grid such that the transducer source/face would be parallel to the skull at a desired point?</p> <p>Thank for taking the time to field these questions.<br /> An aside, this is all for neuroresearch at Arizona State. If you have the time to discuss more on phone/Gchat, we would be happy to collaborate on this (jmfine@asu.edu). </p> <p>The end game is to actually use the 4channel system, calculate the distortion, then correct for it with the phased array. </p> <p>Justin Fine, PhD. </p>