Question concerning 'Start Recording'

[grova]

Hello everybody,

To produce summary data for a clinician, we created a fusion image (anatomical MRI + fMRI t map) and we would like to save a list of .jpg images of that fusion data every 5 mm.

Two questions :
- I used the 'start recording' / 'stop recording' function to create a list of .jpg files and I just use 'space' to get all the 1 mm slices : would it be possible to do the same but with a greater step between slices (e.g. every 5 slices) ?

- we were using the last version of anatomist under windows 2000, we obtained a strange result ... every jpg file showed a strange blue background .... any idea ??? (NB: with the same data, the result was perfect under linux)


Thanks in advance

Christophe

[Guest]

Hi,


This strange things about blue background is known and Denis have corrected it for next paketage. This things is only with windows.

You can create a image serie with a step of 5 mm. You can use BrainVISA with advanced level (Preferences -> General -> UserLevel ). And then ....

ETAPE 1:

- locate at animation module

- choose 'Anatomist record animation' and open it

- clik on 'Directory' and indicate a name for animation. For instance, animation.banim. Don't forgot .banim extension

- Choose a type windox, for instance 'Axial'.

- Click 'Run' and BrainVISA will launch Anatomist

- Place your image in window

- Indicate number of step, by defaults is 100. For instance if you have 180 slice of 1 mm, you can put 36!

- Click on 'ok' to begin animation

- Click on space key to see images

- Clcik on 'ok' to stop animation

- Click on 'stop' to stop brainvisa treatement.



ETAPE 2 :


- choose 'Anatomist view animation' and open it

- indicate your .banim in 'anim'

- indicate window (i.e. axial)

- use_recorded_objects : true

- keep_images : true

- Give a image basename (often there is a default name, you can change it if you want)

- mpeg_file must be empty (you made images and not film)

- encoder is empty

- all others parameters are by default.

- You can click 'Run' ! (you must put image in window when Anatomist is launched and click 'OK')

Isabelle

[grova]

Thank you Isabelle for your answer, I would have 3 more questions :

- when will the new windows release, with the bug concerning the blue background fixed, be available ?

- when using the Record animation software, I don t understand very well the meaning of the number of steps ? Moreover, it is written than fusion images could not be included in such animation, am I right ?

- Finally, as I really need to create those fMRI/MRI fusion jpegs soon, and on many patients, would it be possible to use some command lines to do that ? In other words is there any way to put a fusion image as the input of AimsData2Jpeg ??

Thanks in advance for your help

Christophe

[denghien]

Hello,

I don't know exactely the date for a new paketage but I think around at the beginning of the year 2005.

number of steps : it is the number of 'snapshot' images of your film - it is like a sampling.

Fusion images : it seems to me you can made it if you create images fusion manually and if you load it in the windows before clik ok ('Animation view animation' proccess).

Fusion image and AimsData2Jpeg : In fact you can create one image of fusion with AimsLinearComb command and then you can use it.


Isabelle

[riviere]

Hi Christophe,

For the color bug on Windows, I think (I don't remember exactly and I will check) that I have fixed it on the stable branch of our libraries, this means that it will be part of the next stable version update. I don't know when I will have time to release a new Windows package because I don't work on Windows regularly but it can be quite fast (before the next version planed approximately at the end of year or beginning of 2005).

The steps parameter of RecordAnim is the number of images that will be generated between two consecutive points of view. The slice position is interpolated in consequence.
Fusions are not re-created by the ShowAnim process so you will have to do it by hand, or do something else.

Something else:
You can use anatomist remote-control (or script) interface to make it do what you want. You can use commands to load and display objects in anatomist, make fusions, snapshots etc. They are documented in french, but, how lucky you are, you happen to speak french: see http://brainvisa.info/doc/html/anatomis ... mands.html.
These commands can be executed by 4 ways:
- load a commands script file (.ana) like an object in anatomist (using the "open" icon or menu, or start anatomist with the .ana file as argument)
- use a named pipe to pilot anatomist:

Code: Select all

mkfifo pipe
anatomist -p pipe &
cat >> pipe
<type commands>

- use a network socket:

Code: Select all

anatomist -s 50000

will open anatomist in server mode and listen to connections on port 50000. Then you can open a connection (using telnet for instance) to anatomist. This is how brainvisa controls anatomist.
- make a BrainVisa process script: Anatomist commands are wrapped in python and you can directly and easily do many things, see the Anatomist.py file and class, and examples in viewer processes.

AimsData2Jpg is an old command and only deals with one image, sorry...

Denis