EMSegment Command-line Target Volumes

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hum
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EMSegment Command-line Target Volumes

hum
Hi all,

I'm trying to use the EMSegment Command-line Interface to segment several
brain MRI cases with atlas. I'm using MRI-Human-Brain-Full-Parcellation.mrml
as the MRML scene defining the task and EM_Map.nrrd as the result labelmap.
I wish to add several target volumes at once (to avoid running the
EMSegmenter with Atlas module for each case) but it is not allowing me to do
so. The documentation at
http://www.slicer.org/slicerWiki/index.php/Modules:EMSegment-Command-Line3.6
explains that multiple files can be selected at once. Is this not possible
anymore for the 4.5 version of Slicer? If so, what other options do I have
to run the segmentation in a batch of cases?

Also, when I tried running the module with one target volume, the status was
'completed with errors'. The error shown in the log was 'MetaImage: Read:
Cannot open data file.' The EMSegmenter with Atlas module could open .mhd
files, I assumed it would be the same for the Command-Line Interface. Do I
need to first convert the file to a .nrrd format?

Thanks so much,
Hyemin



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Re: EMSegment Command-line Target Volumes

Kilian Pohl
See comments inline

On 12/13/2016 8:24 AM, hum wrote:
> Hi all,
>
> I'm trying to use the EMSegment Command-line Interface to segment several
> brain MRI cases with atlas. I'm using MRI-Human-Brain-Full-Parcellation.mrml
> as the MRML scene defining the task and EM_Map.nrrd as the result labelmap.
> I wish to add several target volumes at once (to avoid running the
> EMSegmenter with Atlas module for each case) but it is not allowing me to do
> so.
you can only run the module one case at a time . If you want to run it
in batch mode you might want to try running it as a  command line tool
>   The documentation at
> http://www.slicer.org/slicerWiki/index.php/Modules:EMSegment-Command-Line3.6
> explains that multiple files can be selected at once. Is this not possible
> anymore for the 4.5 version of Slicer? If so, what other options do I have
> to run the segmentation in a batch of cases?
this is relates to have multiple input channel of the same subject (e.g.
T1 , T2 ...)
>
> Also, when I tried running the module with one target volume, the status was
> 'completed with errors'. The error shown in the log was 'MetaImage: Read:
> Cannot open data file.' The EMSegmenter with Atlas module could open .mhd
> files, I assumed it would be the same for the Command-Line Interface. Do I
> need to first convert the file to a .nrrd format?
That might be the case - try converting to nrrd file first

Kilian

>
> Thanks so much,
> Hyemin
>
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/EMSegment-Command-line-Target-Volumes-tp4031437.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

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