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 <mthuerl...@web.de> Organization: http://freemail.web.de/ To: Donna Dierker <do...@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" <do...@brainvis.wustl.edu> > Gesendet: 06.04.09 17:45:30 > An: Markus Thuerling <mthuerl...@web.de> > CC: John Harwell <j...@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 > > > > > > > > ____________________________________________________________________ > > Psssst! Schon vom neuen WEB.DE MultiMessenger gehört? > > Der kann`s mit allen: http://www.produkte.web.de/messenger/?did=3123 > > > > > > > > ------------------------------------------------------------------------ > > > > > > ------------------------------------------------------------------------ > > > > ________________________________________________________________________ Neu bei WEB.DE: Kostenlose maxdome Movie-FLAT! https://register.maxdome.de/xml/order/LpWebDe?ac=OM.MD.MD008K15726T7073a _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
