MRI segmentation using morphologist 2015 error

Questions about BrainVisa usage and installation

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AlejandroBP
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Joined: Wed Jun 06, 2018 4:01 pm

MRI segmentation using morphologist 2015 error

Postby AlejandroBP » Fri Jun 15, 2018 7:41 pm

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

AlejandroBP
Posts: 8
Joined: Wed Jun 06, 2018 4:01 pm

Re: MRI segmentation using morphologist 2015 error

Postby AlejandroBP » Fri Jun 15, 2018 7:53 pm

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

willsnyder12
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Joined: Tue Jun 05, 2018 6:34 pm

Re: MRI segmentation using morphologist 2015 error

Postby willsnyder12 » Thu Jun 28, 2018 1:14 pm

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

willsnyder12
Posts: 11
Joined: Tue Jun 05, 2018 6:34 pm

Re: MRI segmentation using morphologist 2015 error

Postby willsnyder12 » Thu Jun 28, 2018 1:15 pm

**Correction: brainvisa MRI (not mdi) format

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riviere
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Re: MRI segmentation using morphologist 2015 error

Postby riviere » Thu Jun 28, 2018 1:28 pm

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

AlejandroBP
Posts: 8
Joined: Wed Jun 06, 2018 4:01 pm

Re: MRI segmentation using morphologist 2015 error

Postby AlejandroBP » Thu Jun 28, 2018 5:36 pm

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.

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riviere
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Re: MRI segmentation using morphologist 2015 error

Postby riviere » Thu Jun 28, 2018 5:52 pm

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

AlejandroBP
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Joined: Wed Jun 06, 2018 4:01 pm

Re: MRI segmentation using morphologist 2015 error

Postby AlejandroBP » Fri Jul 06, 2018 10:42 pm

Thank you again Will and Denis,

Despite the small error everything seems to be there.

Thank you sincerely

Alejandro


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