segmentation error with AimsFileConvert

[denghien]

Hi,


I don't understand a problem about conversion file because I can view correctly an image with Anatomist but when I want convert this image (.vimg) to GIS format then I obtained a error of segmentation :

Code: Select all

denghien% AimsFileConvert -i anat.vimg -o anat.ima
filein  : anat.vimg
fileout : anat.ima
ascii   : 0
rescale : 0
format  :
type    :
objtype :
xdim    : 0
ydim    : 0
zdim    : 0
reading anat.vimg as Volume / S16...
Unknown allocation method
Incident de segmentation

Here is the .vinfo

Code: Select all

denghien% AimsFileInfo anat.vinfo
attributes = {
    'file_type' : 'VIDA',
    'byte_swapping' : 0,
    'volume_dimension' : [ 256, 256, 124, 1 ],
    'voxel_size' : [ 0.9375, 0.9375, 1.2 ],
    'time_resolution' : 1,
    'data_type' : 'S16',
    'object_type' : 'Volume',
    'possible_data_types' : [ 'S16', 'FLOAT' ]
  }

Does anyone know this problem ?

Isa

[Jean-Francois Mangin]

If it is urgent, you can try VipConvert, you may be lucky. Of course, we have to understand what happens in Aims library.

[denghien]

Hi ,

Thanks, it was no very urgent. But I tried VipConvert too and I obtained this message :

Code: Select all

denghien% VipConvert -i anat -o anatGis -r t
ncopen: filename "anat.mnc": No such file or directory
miopen: MINC package entry point
ncopen: filename "anat.mnc": No such file or directory
miopen: MINC package entry point
Unknown allocation method
read aimsdata: 256, vol: 256, border: 0
denghien%

I understand why it looks for anat.mnc ... With the person who gave me this image, we put the original file and we obtained the same. But this person tell me what this image has been converted into an other format! And the converiosn for others similar images works. Perhaps there was a reconstrution problem or something like that .... I will check this with raw data.

Isa

[Jean-Francois Mangin]

I do not know exactly what happen, but now that Vip I/O have
been replaced by AIms I/O (through a link), I guess the problem is similar. I was just trying to check if the problem stem from the I/O module.

In fact, it is strange that Vip is trying to open a minc image, because according to Vip syntax,
you force the lecture of a GIS/Tivoli format...

[Yann Cointepas]

This problem is related to the new allocation system for volumes which is in cartodata. This system is used by both Vip and Aims. What I don't understand is why it is working in Anatomist ? It is supposed to use the same reader library... A closer look to the sources is necessary.

[Yann Cointepas]

I may have been wrong in my previous post. The message "Unknown allocation method" does not seem to be an error message. It must be a debug message.

[riviere]

Hi,

The message "Unknown allocation method" does not seem to be an error message. It must be a debug message.

It's both a debug message and an error message: it is an error stemming from a bug.
There was actually a bug in the allocators handling in the Vida reader. It's fixed in Aims 3.0 (perforce).

Vip and Aims now use the same IO system, so inherit the same bugs, that's the improvement of modernity

Denis