Hello Donna, thanks for your great help. I used the link to upload the compressed file university_duisburg_essen.zip. This contains two folders. The first, named as original files, contains the old SWI_Images (img/hdr format in which the conversion was not possible - either the voxel size growth from 0.5x0.5x0.5mm^3 to 1x1x1mm^3 or in CARET the offset occurs) and the old nucleii from the cerebellum in the nii-format. The second (named as my_corrected_files) was formed with the software SUIT_Isolate (this was developed from Joern Diedrichsen to isolate the cerebellum) to get smaller files (reduced the size from 45 megabyte to 25 megabyte). Here it was possible to convert the img/hdr- to nii-format without problems (i don't no why). I must open the nucleii-files in MRICRON under draw\open voi and saved it again to avoid offsets in CARET. So problem 1 could be solved, but i cannot explain it. With the steps in CARET that i told you in the first email to get the surface from the nucleii i got the same problem, that the surface is only gray at one part of the surface of the nucleii. The OUT OF MEMORY-problem occurs sometimes in SPM. It is usual to use such great files in CARET?
PS: It could be that i see your emails one day later because the time lag between Germany and USA. ;) Best regards Markus > -----Ursprüngliche Nachricht----- > Von: "Donna Dierker" <do...@brainvis.wustl.edu> > Gesendet: 06.04.09 21:07:10 > An: caret-users <caret-users@brainvis.wustl.edu> > Betreff: [caret-users] [Fwd: Re: Problems with CARET] > 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! 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