BrainVISA

Good afternoon,
I have been trying to segment an MRI using Morphologist 2015 in brainVISA. However, I keep on getting the following error. I tried different brainVISA version on different two different computer, as well as choosing different MRI, same error.

Here is what I am doing.
First I am converting my MRI (dicom) into nifti format using MRIConvert.
Using Morphologist 2015, I import the MRI (nifty format) into t1mri.
Using the Anatomist option of t1mri, I identify the AC, PC, IH and LH.
In t1mri_nobia, I chose gz compressed NIFTI-1 image (for file format) and I put a subject name (e.g. aa01), all the other options I keep them to “any”
In image orientation handling, I chose the commissure coordinated from the database.
When I hit “run”, Image orientation handling goes fine, but I get an error at the second step (T1 Bias Correction).

-----------------------------------------------------------------------
Here is the following error I get :
-------------------------------------------------------------------------- !! VIP Error: S16BIT type ------------------------------ ------------------------------ !! VIP Error: Execution aborted in function '(brain)VipPutOneSliceTwoZero'. ------------------------------ ------------------------------ !! VIP Error: S16BIT type ------------------------------ ------------------------------ !! VIP Error: Execution aborted in function '(brain)VipPutOneSliceTwoZero'. ------------------------------ ------------------------------ !! VIP Error: S16BIT type ------------------------------ ------------------------------ !! VIP Error: Execution aborted in function '(brain)VipPutOneSliceTwoZero'. ------------------------------ ------------------------------ !! VIP Error: S16BIT type ------------------------------ ------------------------------ !! VIP Error: Execution aborted in function '(brain)VipPutOneSliceTwoZero'. ------------------------------ ------------------------------ !! VIP Error: S16BIT type ------------------------------ ------------------------------ !! VIP Error: Execution aborted in function '(brain)VipPutOneSliceTwoZero'. ------------------------------ ------------------------------ !! VIP Error: S16BIT type ------------------------------ ------------------------------ !!
in T1 Bias Correction 1 System command exited with non null value : 111
________________________________________RuntimeError

in Morphologist 2015 1 System command exited with non null value : 111
________________________________________RuntimeError
--------------------------------------------------------------------------

If someone has an idea where is the problem or any help would be greatly appreciated.

Thank you

Alexjandro

I'm sorry again, but I forgot to add that I also tried to use the original DICOM files into brainVISA directly, as well as converting them into BrainViSa MRI format, but I also get a similar error.

thank you

Hi Alexjandro,

I've had similar problems before. When you converted to brainvisa mdi format, did you set the voxel type to S16? Try using the Aims Converter tool in BrainVISA (Tools>converters>Aims Converter) and select the output voxel type to be S16. This helped with some errors in the past I have encountered.

Best,
Will

**Correction: brainvisa MRI (not mdi) format

Hi,
Have you used the T1 MRI importation process before running morphologist ? Normally this process takes care of all conversions for Morphologist.
If it still desn't work, then there is a "real" problem...
Denis

Thank you Will and Denis,

I tried them and for once it went "well" all the process in Morphologist 2015 without any "red cross/errors next to each processes" (basically all steps were "green checked". In other words, the segmentation went threw (well).

However, I get only one "error message" this times at the beginning of the segmentation.

------------------------------ !! VIP Error: Negative or NULL limit value! ------------------------------ ------------------------------ !! VIP Error: Execution aborted in function '(distmap)VipComputeFrontPropagationConnectivityDistanceMap'. ------------------------------

Is it an error I should be worried about? what does it mean?.


Thank you again so much for your help.

It depends on he context
Well morphologist often outputs this kind of messages in a non-harmful way. If the process goes to the end and produces readable results, then it is OK. I admit that the messages are misleading...
Denis

Thank you again Will and Denis,

Despite the small error everything seems to be there.

Thank you sincerely

Alejandro