Hi Donna,
Thanks for your help. I am sending you two histograms of 3D_resliced.nii:
(1) histogram_resliced_1.jpg is the same histogram you already sent to me;
(2) histogram_resliced_2.jpg is the histogram of 3D_resliced.nii after
resampling at 1x1x1mm with Caret.
We can see that the spikes disapear in (2). It looks like much closer to
the histograms described in your 'Peak Tweaking' document. As I don't
have much experience with image segmentation, I was wondering if there
was any problem with my images. I am glad to know that they look fine
for you.
May be the problem is the one pointed by Simon. If this is the case,
adjusting the histogram bins could minimize the effect. Do we have
control over the histogram bins with Caret interface?
Thanks,
Mateus
Dierker wrote:
Hi Mateus,
I can't address your original problem with the NIfTI
orientation/rotation, but I did have a look at your volumes, and this
statement confuses me:
The histogram of my images (3D_original.nii and 3D_resliced.nii)
shows several noisy sharp peaks.
The attached captures show the histograms of 3D_original.nii
(histogram_orig.jpg) and 3D_resliced.nii (histogram_resliced.jpg).
The original has smoother looking peaks, but both have discernible
gray and white matter peaks. Neither look particularly bothersome.
Could you be more clear about what concerns you?
On 11/13/2006 05:43 AM, Mateus Joffily wrote:
John,
May I profit from the fact that I have already uploaded my images to
ask you one more question about them? The histogram of my images
(3D_original.nii and 3D_resliced.nii) shows several noisy sharp
peaks. Do you know what do they mean? I know that, if I reslice the
3D_resliced.nii to 1x1x1mm voxels size with Caret, they disappear.
Thanks.
Mateus
John Harwell wrote:
Hi Mateus,
Can you upload the nifti volume that is not displayed correctly in
Caret at http://pulvinar.wustl.edu/cgi-bin/upload.cgi;. Also, can
you capture and upload an image of the volume displayed correctly
in SPM5 so that I know how it should appear.
After uploading the files, please email me the names of the files.
It may be a few days before I can look into this problem.
--
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110 USA
On Nov 10, 2006, at 9:42 AM, Mateus Joffily wrote:
Hi,
I am having some trouble to load nifti images with caret5. The
problem is the following:
1) When I try to load an image that has a rotation specified in
the header, Caret seems not to apply it properly. The displayed
image shows a strange orientation and the voxels size is wrong.
2) However, when the same image is resliced and no rotation is
specified in its header, Caret displays the image correctly, the
voxels size are correct and the image origin is also correctly
located.
Those same images, (1) and (2), are both correctly displayed with
SPM5.
The images extension is .nii, so I don't think this should be a
problem related to image format interpretation (like interpreting
nifti images as analyze and ignoring part of the header information).
Does anyone else has experienced this problem? Thanks for your help.
Mateus
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inline: histogram_resliced_1.jpginline: histogram_resliced_2.jpg
