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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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
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