BrainVISA

Hi Denis, I'm working on a pyanatomist script in order to create a fusion2Method between a lot of ROIs (12) and a T1 template. It works correctly, but the mixing rate is very automatically low because of the number of ROIs. So the opacity of ROIs is very low. Then I would like to set up the paramete...

Hi,

I suppose you use pyanatomist ?
Take a look at http://brainvisa.info/doc/pyanatomist-4 ... _base.html and search "hiddenface_wireframe" .

Isa

Thanks Denis, 1) It's exactly what I need. 2) My user case is the second. I want to load an identity transformation between 2 referentials as in the anatomist GUI by using "Ctrl + left button". So I wonder if there is a magic parameter or function instead of using something like a.loadTran...

Hi Denis, I have written a pyanatomist script in order to create many fusions between anatomy and map activation. It works but : 1) I have a problem with the settings of palette. The value min and max (set in the script) are not the same when the GUI of Anatomist is launched, I suppose that Anatomis...

Hi, If you use the "reduction_reference_factor" (it works on reference image), you will damage the image. For example, if you choose the value "1", then 1 voxel out of 2 in the 3 directions will be damaged. It is interesting if images doesn't have the same modality in particular ...

Hi, You could find some information on this part of documentation (Aims command line): http://brainvisa.info/doc/aimsdata-4.3/aims_training/en/html/ch08s02.html In fact, Brainvisa interfaces the AimsMIRregister command line, which is usable in a terminal too. If you launch : AimsMIRegister -h, you w...

Hi Joost,

You will find some examples in this part of documentation at the "Meshes" section:
http://brainvisa.info/doc/aimsdata-4.3/ ... ing%pyaims .


Isa

Hi, In fact you can't use AimsMIRegister in order to compute an affine registration. Sorry, "AffineTransformation3d" mention has been written by default in the help, but it is an error. AimsBlockMatching command is available to compute an affine registration but set the --transfo option to...

Hi, I suppose you used AimsMIRegister then AimsResample in order to obtain your result, isn't it ? You can use some options with the AimsResample command to change the size of the output. These options are the following: [ --dx <S32> ] dimx of the resampled volume [ --dy <S32> ] dimy of the resample...

Hi, With this kind of error message, it seems a problem has occurred during the update of database. And in this case, the database stays in a "locked" state. I suppose that you have a file something like <journal...> in the root directory of freesurfer database which has been written by Br...

Hi, In order to fill out form automatically, you must: 1) create a database (http://brainvisa.info/doc/axon-4.3/bv_training/en/html/ch02s04.html) 2) import data in this database ( http://brainvisa.info/doc/axon-4.3/bv_training/en/html/ch03s02.html ) After that Brainvisa can fill out all parameters w...

Hi, I've looked at your log and I suggest that you check a few points : -> Can you visualize correctly the following data "../experiments/bv_database2/prot1/OAS1_0001_orig_001/t1mri/acq1/normalized_norm1_OAS1_0001_orig_001.nii" by clicking on the eye in the brainvisa GUI ? -> Have you sele...

Hi,

In fact, if the input image is a .nii format, I don't know why it tries to convert into tiff.
Could you post a snapshot ?

Thanks,

Isa

ok
I'm going to reply by email.
Isa

Could you please send us some snapshots of the result and the data ?
Thanks,