drawing ROI on anatomist

[aurely1310]

Hello,

I have some problem with the ROI on anatomist : I can not draw it!

As said in the manual, I did these steps :

- I choosed my file in the database in BrainVisa, using the button "ROI drawing".
- I ckicked on the "eye" to open it on Anatomist.
- Then, i pushed F1 to get the main setting window (with "paint" and "ROI")
- On ROI, I created a new session and new region.

- Then I choosed "axial" and a window with my image appeared. I pushed the bushon "paint".

Normally, I'm now able to draw the ROI, but when I want to do it (click on the left button), nothing appears on the picture!

Could you help me please??

Thank you very much,
aurely1310.

[Dominique Geffroy]

Hi,

Indeed it seems there is a problem with the feature "painting views" in the Roi Management panel, which you used to open an axial window. You can try drawing directly in the first window you opened without using the axial button to open another window.

However, I didn't understand what you did with Brainvisa before trying to draw ROI. Did you use the process tools -> ROI Drawing ? In this case, you shouldn't have had to do all that steps manually (open the roi management windows, creating a session, a region...), this process have a "Show" button that do that for you. Moreover, it enables drawing in a block of 4 views window which is more convenient for the drawing.

Dominique

[aurely1310]

Hello Dominique,

Thank you for your answer.
You're right : before trying to draw ROI, I opened the window "ROI Drawing" in Brainvisa.
Then, I selected the file and clicked on the button "show".

The window with my image appears. I can do nothing on it (can not draw).
And when I select the paint button, I can see the "main setting" window...

I try to do it manually but impossible to draw something on the picture...

How can I do, please?!

Thank you very much,
aurely1310

[Dominique Geffroy]

Hi Aurely,

I don't understand why it doesn't work when you use the Brainvisa "Roi Drawing" process. I've just tested it, it works well.
Maybe you could send a screen copy of what you've done...

Anyway, you can draw ROI directly with Anatomist. If you follow the steps described in Anatomist tutorial, it should work : http://brainvisa.info/doc/anatomist-3.2 ... /ch05.html
Only the feature "Painting views" in Roi management panel is broken, but if you don't use it, you shouldn't have problem to draw ROI. This feature will be repaired in the next version of Anatomist.

Dominique

[riviere]

Hi,
For the problem on windows opened from Anatomist ROI panel, I think it was "just" that ROIs were not added in the new windows; the user had to select them again in the ROI selection panel. It will be fixed in the next version.
For the "ROI drawing" process in BV, Aurelie I think you didn't use it the right way: you speak about the "eye" icon, which you shouldn't need to use in the ROI drawing process. Did you select a ROI file (*.arg file) in the ROI parameter ? (it can be a non-existing file)

Denis

[aurely1310]

Hello,

In fact in BV I selected the source (raw T1 MRI) and then clicked on the "eye" button.
- Then I HAVE TO CLICK on ROI (no automatic opening).
- I HAVE also TO CREATE the session and region because nothing is filled in!
- After that, I change the brush size
- Now, I can draw the ROI on my raw T1 MRI.


Then I did the only possibility : i saved the result manually an import it (.arg) on the second line (ROI) of the window "Dessin de ROI".

After selecting "Execute", the next step opens the window shown in the online help (see joined picture :

ROIwindow.jpg (94.42 KiB) Viewed 8555 times

) and I don't know what to do!
When I confirm the ROI, an exception in announced :



dans Dessin de ROI 2 maximum recursion depth exceeded

RuntimeError
neuroProcesses.py (1834) in _processExecution: result = process.execution( self )
ROIDrawing.py (96) in execution:
regionsObject.save(self.ROI.fullPath())
threadedimpl.py (109) in <lambda>:
return lambda *args, **kwargs: mainThread.call(func, *args, **kwargs)
qt3thread.py (189) in _callAndWakeUp:
semaphore._mainThreadActionResult = function( *args )
base.py (1185) in save:
self.anatomistinstance.execute("SaveObject", object=self, filename=filename)
threadedimpl.py (109) in <lambda>:
return lambda *args, **kwargs: mainThread.call(func, *args, **kwargs)
qt3thread.py (160) in call:
return apply( function, args, kwargs )
api.py (780) in execute:
return self.theProcessor().execute(command, **params)
__init__.py (441) in newexecute:
replace_dict( dic, cc )
__init__.py (393) in replace_dict:
replace_list( v, cc )
__init__.py (408) in replace_list:
replace_list( v, cc )
__init__.py (408) in replace_list:
replace_list( v, cc )
__init__.py (408) in replace_list:
replace_list( v, cc )

What can I do?

Thank you very much,
Aurélie.

[riviere]

In the ROI drawing process, the ROI .arg does not need to exist: you can type a .arg filename which doesn't exist yet: it will be the output of the process. Then you don't need to click on the eye icon: the "show" button of the ROI drawing process should take care of loading everything needed in Anatomist, creating or loading the ROI session and ROI objects, opening suitable views, and setting Anatomist into drawing mode.
Then I don't have the error you get when confirming, maybe it's a consequence of something happening before, but I am not able to reproduce it right now. Which system are you using ? Windows ? Linux ?
Denis

[aurely1310]

Hello,

I'm sorry to be too long to answer, but I forgot to suscribe to the topic!

I'm working on Windows.

I tried like you said (ideally I don't want to open anatomist separetely): juste write "ROI_test.arg" in output and launch the application.
I get the same error as said before...

I tried another way : instead to just write the name, i tried also to click on

BDDsortie.jpg (999 Bytes) Viewed 8538 times

(seletion of "ROI" in the field "data type").

But I always have the same error...
I hope you'll be able to help me, please!

Thank you very much,
Aurélie.

[Dominique Geffroy]

Hello,

Indeed, the error you get is due to a bug, that occur only on Windows version. It will be corrected in the next version of Brainvisa, which should be available soon (before the end of may I hope).
Meanwhile, you'll have to draw ROI directly with Anatomist without the help of the Brainvisa Roi drawing tool.

Dominique