Import MINC data

[as_dub]

Hello,

I would like to import MINC data in BV, but when I run the import function (data managment -> anatomy -> Import T1 MRI) the converter doesn't recognize MINC format. I get this error :

D:\AnneSophieDubarry\SHFJ_pack-stable-win32-3.0.1\bin\commands-links\AimsFileConvert.exe: D:\AnneSophieDubarry\DATA\brainvisaData\protocoleLangage\E01VF_MINC\MINC\e01vf_20031006_080554_3_mri.mnc : unrecognized format

dans Importation d'une IRM T1 1 RuntimeError: Commande système terminée avec une valeur non nulle : 1

neuroProcesses.py (1612) in _processExecution:
result = process.execution( self )
ImportT1MRI.py (142) in execution:
context.system( *cmd )
neuroProcessesGUI.py (932) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (1692) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

Does anyone can help me please ? Thank you,

Anne-Sophie

[Jean-Francois Mangin]

I think to be able to do that, you need to have minc libraries somewhere (depending on the system you use). We do not distribute it in our package, we just have
a system pluging in minc Input/Output when required. Furthermore, I think you need a specific version, probably minc 1.3.

Here I have no problem importing minc files in brainVISA.

Of course, I may be wrong, but the wizard in slying in the Alpes...

[riviere]

Hi,

Normally the Minc libraries are shipped with the binary package (I think they are statically linked in the minc plugin of Aims) so they should work.
I remember having tested them on Windows a long time ago just after Olivier Coliot wrote the Minc plugin, but maybe they broke down after that...
Can you try reading the same image on a Linux version and tell us if it makes any difference please ?

Denis

[as_dub]

Hello,

I tried to read the same image on Linux and it works well. So something may have happened since you tested it. Or I did something wrong way..
Thank you !

[Olivier_Colliot]

Hi,

Just to mention that I also have a problem when importing under Windows.
However the error message is a bit different:

Code: Select all

ncopen: filename "D:UsersColliotTransferttrashBERg_tal.mnc": No such file or directory 
miopen: MINC package entry point 
DcmElement: Unknown Tag & Data(0000,0a00) larger (50331648) that remaining bytes in file 
DcmItem: Dataset not in ascending tag order, at element (0000,0a00) 
C:\SHFJ\SHFJ_pack-stable-win32-3.0.0\bin\commands-links\AimsFileConvert.exe: D:\Users\Colliot\Transfert\trash\BERg_tal.mnc : unrecognized format 

The first 4 lines where not in your error message. I have the impression that the windows backslash characters are not read correctly.

However, I have no problem when I read minc files using the aims plugin outside BrainVisa.
For example, it works fine under Anatomist or when using AimsFileConvert from the command line.
Maybe BV does not handle the backslashes correctly when a MINC file is loaded (which is a bit surprising since it handles them correctly for other file formats)