This is the main wiki page for labs in Medical Imaging Systems (codes BAM33ZSL, BEAM33ZSL, A6M33ZSL). Practical ultrasound Practical ultrasound
Teaching assistants:
Labs take place on Wednesdays at 11:00 or 12:45, in room KN:E-132 (Karlovo nám.).
The title in italics means there is no session in the computer lab - it is either elsewhere or canceled.
The materials (or their final version) will be provided before each lab session.
| No. | Date | Lecturer | Topic | Homework | |
|---|---|---|---|---|---|
| 1. | Wed 22.2. | JA | Introduction, Matlab, statistical test | Introduction, hypothesis testing | |
| 2. | Wed 1.3. | JS, JA | Guided visit to Motol hospital imaging facilities, fMRI acquisition | Microscopy | |
| 3. | Wed 8.3. | JS, JA | Guided visit to Motol hospital imaging facilities, fMRI acquisition | Segmentation using thresholding and morphology | |
| 4. | Wed 15.3. | JS, JA | Guided visit to Motol hospital imaging facilities, fMRI acquisition | Ultrasound theory I | |
| 5. | Wed 22.3. | JS, JA | fMRI processing 1. Please install SPM12 and download the data before the lab. On the lab computers, SPM12 is installed in /opt/MATLAB/spm12 and it is enough to add the path. | ||
| 6. | Wed 29.3. | JS, JA | fMRI processing 2 | fMRI homework | |
| 7. | Wed 5.4. | RJ | Voxel-based analysis - detection of hypometabolism in positron emission tomography (PET) | Data for PET, data for brain segmentation and brain volume estimation and live script for the lab, that will also be the homework. 3D Slicer can be used for the visulization of the data, see the tutorial video. | |
| 8. | Wed 12.4. | JA | Ultrasound simulation and reconstruction | Ultrasound simulation and reconstruction | |
| 9. | Wed 19.4. | JA | CT Radon transform | CT Radon transform | |
| 10. | Wed 26.4. | JK,JH | Practical ultrasound - no class this week in E132 | instructions, reservation table | report from the measurements |
| 11. | Wed 3.5. | JA | CT Filtered backprojection | CT Filtered backprojection | |
| 12. | Wed 10.5. | JA | Rector's day | ||
| 13. | Wed 17.5. | JA | CT Iterative reconstruction | CT Algebraic reconstruction technique | |
| 14. | Wed 24.5. | JA | Test practice, Q & A | Exercises |
We plan for you to perform some practical experiments with ultrasound. You will work in small groups. To accommodate all of you, some of the labs will be done outside of the standard hours and some in Dejvice. Please make groups of 3 people, see the planning page and mark a slot by either adding a comment there or sending me an email.
We are also offering two optional activities. They are not obligatory but highly recommended. If you want to participate, mark it in one of the tables linked below (will appear in due course). This is the first one.
On Wednesday 1.3., 8.3. and 15.3., we will visit the Motol hospital. You will be shown some imaging devices (CT,MRI, nuclear imaging) and you are encouraged to participate in a functional MRI brain acquisition. This acquisition will be part of a research study and you will also be given your data to process them in the following computer exercises. We will go by groups, about 1/3 each week. Please see the planning table. If you are unable or unwilling to go a certain week, please inform me immediately, either by email or by adding a comment to the table. Both the visit and the acquisition is voluntary but I think it is a very interesting and unique experience and I strongly recommend it. The visit is expected to last a couple of hours (e.g. until 2pm). You should be at 11:00 in the “aula ředitelství FNM a děkanátu 2. LF UK” in the hospital. From the Motol metro station, you go straight across a little “square” (with a pharmacy and a small shop). It is not recommended to enter the hospital by other entrances as many passages are currently closed. If you get lost, call dr. Šanda (702 024 204) or myself (608 28 24 42). There will not be enough time for everybody to go to the scanner. If you want to go into the scanner, let me know or mark it in the table.
This is the second optional activity.
On Thursday afternoon, May 4 at 13:00s (6.4., 4.5., 11.5. and 18.5.) at 14:00 (except for 4.5., where we start at 13:00) we will go the General university hospital (VFN) at Karlovo namesti. You will be shown practical clinical ultrasound techniques (B mode, M mode, Doppler, strain…) in small groups and will have the opportunity to try it for yourself.
To get there, take entrance A10 in the main campus, go to the first floor, turn left and find the seminar room (“seminární místnost 3.interny”). At least student from each group should be willing to let himself examined (ideally a male student - female students can also be examined but some examinations, especially of the heart, are more complicated and lead to lower quality images because of the underwear).
Please see the planning table and let me know by adding a comment to the table or by email, which day you want to go.
Na cvičeních budete používat systém Matlab, který sdružuje prostředky pro výpočty, vizualizaci, ladění a programování numerických úloh. Jedná se o široce rozšířeným systémem pro vědecko-technicé výpočty. Je používán na více než 3500 universitách a ve stovkách velkých firem, koukněte např. sem.
Jak ho získat
Matlab není zadarmo. Nicméně studující si mohou doma pro účely studia nainstalovat multilicenci ČVUT Matlabu s pomocí hlavního přístupového hesla.
Jak začít
Předpokládáme základní znalost prostředí Matlab, pokud si znalosti chcete osvojit, doplnit či připomenout, doporučujeme následující tutoriál (cz) a další materiály z webu.
We will use Matlab for computation, visualization and other numerical calculations. Matlab is commonly used tool in research and development from academia to private companies.
How to get it
For study purposes, students are allowed to use the CTU multi-licence of Matlab on their own computers. The main CTU password is required for downloading.
How to start
Please use one of the web tutorials to freshen or improve your MATLAB experience.