[caret-users] File Import issue
Donna Dierker
donna at brainvis.wustl.edu
Wed Jan 30 15:00:58 CST 2008
Excellent -- yes, .nii is safer than .hdr/.img pair, although John might
be working on adding support for NIfTI .hdr/.img pairs. When I loaded
the .hdr/.img in Caret, I replicated your problem immediately, but my
terminal window had this message:
HDR file is a NIFTI header file.
Still, the voxdims were as you report below (0.959 x 1.188 x 0.729*),
and the z axis appeared compressed in the sagittal and coronal views
(see attached capture). I wonder if this is because this is an oblique
volume? When I opened it in AFNI, it said it was.
The fact that the voxdims appear correct and the views are normal when
you open the .nii volume is reassuring, but it seemed worth mentioning,
in case you run into trouble segmenting.
*
On 01/30/2008 02:11 PM, neeru K wrote:
> Dear Sirs,
> I am sorry for the delay in uploading the img file. I have uploaded
> the file with same name IM_0001.img.
> The voxel size of the image is actually 1 cubic mm but when I open the
> 'Edit Volume attributes' option, the voxel size that the software
> takes or shows is 0.959 x 1.188 x 0.729 cubic mm.
> As you had mentioned I saved the file .nii file and it does appear
> normal and the voxel size also matches with that of the original
> values (0.993 x 0.927 x 1.007 cubic mm)
> I will proceed with segmentation now.
> Thank you
> regards
>
>
> On 1/30/08, *Donna Dierker* <donna at brainvis.wustl.edu
> <mailto:donna at brainvis.wustl.edu>> wrote:
>
> Hi Niranjan,
>
> I can't replicate the problem without the .img file, too, but I
> did look
> at just the .hdr, and there were some non-standard things about it
> (e.g., pixdim[0]=-1.0). I wondered whether this might be a NIFTI
> volume
> written as .hdr/.img, which Caret doesn't yet support? If so, try
> writing it as a .nii file, and see if you still have the scaling
> issue.
> (Note that you can always zoom up on the volume, but this gets tedious
> if you have to open the volume often.)
>
> Donna
>
> On 01/29/2008 05:13 AM, neeru K wrote:
> > Dear Sir
> > When I changed the voxel size through the Volume Menu->Edit Volume
> > Attributes, the image appears normal as in case of the tutorial
> > dataset image.
> > I have uploaded the header file by name IM_0001.hdr.
> > Thanking you
> > Yours sincerely
> >
> >
> >
> > On 1/29/08, *John Harwell* <john at brainvis.wustl.edu
> <mailto:john at brainvis.wustl.edu>
> > <mailto:john at brainvis.wustl.edu
> <mailto:john at brainvis.wustl.edu>>> wrote:
> >
> > Hello,
> >
> > Do you know if the voxel sizes are correct? You can view
> the voxel
> > sizes by selecting Volume Menu->Edit Volume
> Attributes. That might
> > cause the image to appear compressed.
> >
> > In any case, you can upload the header and data files at
> > "http://pulvinar.wustl.edu/cgi-bin/upload.cgi
> > ". After you have uploaded the files, send me an email with
> the name
> > of the files.
> >
> > -----------------------------------
> > John Harwell
> > john at brainmap.wustl.edu <mailto:john at brainmap.wustl.edu>
> <mailto:john at brainmap.wustl.edu <mailto:john at brainmap.wustl.edu>>
> >
> > Department of Anatomy and Neurobiology
> > Washington University School of Medicine
> > 660 S. Euclid Ave Box 8108
> > Saint Louis, MO 63110
> >
> >
> >
> > On Jan 28, 2008, at 12:23 PM, neeru K wrote:
> >
> > > Dear Caret users,
> > > I am beginner in Caret and I have a problem with the
> File/import
> > > data option in Caret software. When I import the header
> file of
> > > human T1 from my experiment, the main window displays the
> image
> > > appears compressed in all the three axes. Am I doing
> something wrong
> > > here because the image looks normal when I import the
> header of T1
> > > that is taken from tutorial dataset provided by the Caret
> website.
> > >
> > > Thanks in advance
> > >
> > >
> > > --
> > > Niranjan Kambi
> > > SRF, Neeraj Lab,
> > > National Brain Research Centre
> > > Manesar, Gurgaon-122050
> > > Haryana, INDIA
> > > Ph:+919818654846
> > > _______________________________________________
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> > <mailto:caret-users at brainvis.wustl.edu
> <mailto:caret-users at brainvis.wustl.edu>>
> > > http://pulvinar.wustl.edu/mailman/listinfo/caret-users
> >
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> >
> >
> >
> >
> > --
> > Niranjan Kambi
> > SRF, Neeraj Lab,
> > National Brain Research Centre
> > Manesar, Gurgaon-122050
> > Haryana, INDIA
> > Ph:+919818654846
> >
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> >
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>
>
> --
> Niranjan Kambi
> SRF, Neeraj Lab,
> National Brain Research Centre
> Manesar, Gurgaon-122050
> Haryana, INDIA
> Ph:+919818654846
> ------------------------------------------------------------------------
>
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