Markus, I want to retract two statements:
* "There is definitely something wrong with the NIfTI header in SWI_Images.hdr": Rather than "is definitely", I think "may be" is more apropos. * "mayo_analyze read the header and interpret the pixdim as cubic 1.0": I misread the output. AFNI's mayo_analyze says the pixdims are cubic 0.5. Both Caret and AFNI still show the segmentation volumes misaligned with the anatomical (in the original_files directory -- not in the corrected_files). This remains true. These are very large volumes (364x448x144x4), but my machine loaded all five segmentations plus the anatomical underlay concurrently, with no out of memory problems. I also was able to reconstruct a VTK model from the segmentations without out of memory errors; however, only the biggest object is reconstructed. I don't know of a way to get Caret to reconstruct a VTK model from multiple objects. I dug out these hints, which David passed on last year when doing something similar with subcortical structures: > Generate surface from segmentation, save coord, topo > Compute folding > Surface ROI: threshold nodes with folding > 1 > Dilate selected nodes twice > Smooth selected nodes 100 iters > This gets rid of spikes while preserving main shape features > Save as vtk model Finally, here is a related hint from John Harwell: > To map functional data to the VTK models, "caret_command > -volume-map-to-vtk-model" has been added. It takes as input a VTK > model file, a functional volume file, and the name of one of the > default color palettes. The output is a VTK model file with color > assignments made using the functional volume. Donna On 04/07/2009 11:52 AM, Donna Dierker wrote: > Hi Markus, > > (Besides the list, I'm cc'ing you directly, to see if this reduces the > time lag. The list server delivers within minutes on my end.) > > There is definitely something wrong with the NIfTI header in > SWI_Images.hdr. At first, I thought perhaps the problem was that > Caret doesn't read NIfTI .hdr/.img pairs (but I thought John added > that recently), or that it is an oblique dataset, as AFNI warns: > > *+ WARNING: If you are performing spatial transformations on an > oblique dset, > such as > /tmp/university_duisburg_essen/original_files/439-alle_kerne.nii, > or viewing/combining it with volumes of differing obliquity, > you should consider running: > 3dWarp -deoblique > on this and other oblique datasets in the same session. > > But the fact that both Caret and mayo_analyze read the header and > interpret the pixdim as cubic 1.0 is a clue (see attached mayo_analyze > output, and compare with the attached nifti_tool output). In AFNI, > when I view the corrected 439-alle_kerneneu.nii overlaid on the > c_SWI_Imagestest.nii, they align fine, but when I view > 439-alle_kerne.nii overlaid on SWI_Images.hdr, they do not (captures > attached). > > It looks like SUIT_Isolate is doing more than just converting > SWI_Images.hdr to NIfTI, so you might want to do something less > drastic, but you somehow need to fix the bad .hdr. > > Donna > > On 04/07/2009 05:26 AM, Markus Thuerling wrote: >> 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! 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 >>> >>> >> >> >> ____________________________________________________________________ >> Psssst! Schon vom neuen WEB.DE MultiMessenger gehört? Der kann`s mit >> allen: http://www.produkte.web.de/messenger/?did=3123 >> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
