[caret-users] [Fwd: Re: Problems with CARET]

Mon Apr 6 13:53:12 CDT 2009

This thread got started off-list, before I saw Markus' pending 
caret-users post and approved it.

By forwarding this message to caret-users, I'm putting it on-list, 
because I think the problem will get solved quicker that way.

There are two separate problems:

1. The segmentation and anatomy volumes are not in register; there 
appears to be an offset/translation, even after both volumes are 
converted to NIfTI and reopened/loaded in Caret.

2.  Caret shuts down (out of memory) when reconstructing the 
segmentation into a VTK model (possibly because there is more than one 
object in the segmentation?).

For problem #1, all I can do is have you upload both volumes and 
reproduce the problem here:

http://pulvinar.wustl.edu/cgi-bin/upload.cgi

 I can also use nifti_tool to display the NIfTI header, which might 
yield some clues (e.g., there is a transform specified in one, but not 
the other).

For problem #2, I'm curious what happens if you try Volume: 
Segmentation: Disconnect Islands before reconstructing the segmentation 
into a VTK model.

-------- Original Message --------
Subject: 	Re: Problems with CARET
Date: 	Mon, 06 Apr 2009 18:23:15 +0200
From: 	Markus Thuerling <mthuerling at web.de>
Organization: 	http://freemail.web.de/
To: 	Donna Dierker <donna at brainvis.wustl.edu>

Hello Donna,
thank you very much for the fast answer. I saved the SWI-datas as nii-file. The datas are displayed isotropic and i don't must change the voxel size. But when i do this (1x1x1mm^3 is not coorect, but negligible), the shift also occurs. 
My Volume Segmentations Files have a size of 23 megabyte. But the Out of Memory-Problem not always occur. It was a great problem as i used the Reconstruct into surface - step with more nucleii resp. with more files which contain one nucleus. It is possible to save the nucleii in one file, but then i don't have an idea to color different nucleii (provided that if it is possible).
You can see i am not an expert in CARET ;) 

Best regards Markus

> -----Ursprüngliche Nachricht-----
> Von: "Donna Dierker" <donna at brainvis.wustl.edu>
> Gesendet: 06.04.09 17:45:30
> An: Markus Thuerling <mthuerling at web.de>
> CC: John Harwell <john at brainvis.wustl.edu>
> Betreff: Re: Problems with CARET

> Hi Markus,
> 
> Is it possible to save SWI.hdr as NIfTI, rather than Analyze?  The 
> translation offset is likely due to the fact that Analyze does not 
> provide adequate/reliable origin information.  It also doesn't prescribe 
> orientation information reliably, so you could also have a flip issue 
> and not realize it.  Usually Analyze *does* provide accurate voxel 
> dimensions, however, so I'm surprised you had to correct the voxdims.
> 
> If the .nii and .hdr files have the same dimensions, voxel dimensions, 
> and origins, then it should be possible to copy the header info from the 
> .nii file to the .hdr.  But if they don't, then I'm not sure how else 
> you can get the correct origin info, other than by going back to the 
> original DICOM.
> 
> I'm cc'ing John Harwell about Caret shutting down (out of memory) after 
> reconstructing the .nii segmentation into a solid structure VTK model.
> 
> If by color different nucleii, you mean can Caret parcellate the 
> cerebellum, the answer is no.  Nor can it parcellate the cortex.  (But 
> in the latter case there are "atlas goodies" that help one 
> probabilistically determine where any given node is located.)  But if 
> you mean is it possible to render a node-ROI or node-color mapping that 
> already exists, then the answer is yes.  (I mean find the label: no; 
> render the label: yes.)
> 
> If your NIfTI dentate.nii file has both left and right dentate 
> structures included in the segmentation, then I wonder if this might be 
> causing the out of memory error above (i.e., Caret is used to dealing 
> with single object segmentations).  If Caret does handle multi-object 
> segmentations, then I'm not sure whether it wants to save each object in 
> its own file, or can support storing multiple objects in a single VTK 
> file.  This is another good question for John.
> 
> Donna
> 
> On 04/06/2009 10:26 AM, Markus Thuerling wrote:
> > Dear Sir or Madam,
> > i am PhD student at the University Duisburg-Essen, Department of Neurology.
> > I want to show the surface of the nucleus dentatus in the cerebellum with CARET v5.61. My problems are shifts between the anatomical volume (the cerebellum was measured with a SWI sequence, saved as hdr / img-file) and the segmentation volume (the dentatus, saved in a nii-file), the right part of the dentatus (and the same problems with other nucleii) is only saved and i want to color different nucleii.
> > I used CARET with the following steps:
> > File\Set Current Directory
> > File\Open Data File\SWI.hdr as Volume Anatomy File
> > Create a spec file with structure cerebellum or all and unknown space (are these inormations important?)
> > Without radiological orientation
> > File\Open Data File\dentate.nii file as Volume Segmentation File
> > Change under D/C the Primary Overlay to Segmentation
> > Volume\Segmentation\Reconstruct into Surface\Solid Structure VTK Model (or Brain Model Surface)
> >  to get the Surface of the nucleus. This step is problematic, because CARET often shut down (Out of Memory) or don't realise this step. I must often repeat open the Volume Anatomy File to get the Model SURFACE&VOLUME.
> > The SWI-image file is not correct displayed so i changed the voxel size to 0,5x0,5x0,5mm^3 (the correct voxel size). 
> > After this step i have a shift between  Anatomy and Segmentation File.
> > It is possible to color different nucleii?
> > In the appendix you can find two screenshots. You can see a gray and a red nucleus. When i want to save the files, or use the procedure to the next nucleus, CARET saves ONLY the right nucleus and i can not explain why. 
> >
> > Thank you in advance Markus Thürling
> >
> >
> >
> > ____________________________________________________________________
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> 

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