Hi John,
Although the image orientation is fine and the origin is correctly
localized at the AC, it still seems to have some problem with the image
dimension and voxel size.
The correct image dimension and voxel size are 201 x 151 x 124 and
-0.938 x 0.938 x 1.3 (X x Y x Z), respectively (see the
3D_original_spm5.pdf file that I uploaded). However, the values
reported by Caret are 124 x 201 x 151 and 1.3 x 0.938 x 0.938.
Thanks for your help,
Mateus
John Harwell wrote:
Mateus,
To download updated versions of Caret:
1) Go to the website "http://brainmap.wustl.edu/pub/john/";. Use the
username "pub" and the password "download" to access the web site.
2) Download the file caret5_exe_linux.zip or caret5_exe_windows.zip
which contain the linux and windows versions of the caret5 executable.
To install:
1) Go into your Caret installation's "bin" directory and backup
(rename) your current caret5 executable.
2) Place the downloaded file in the Caret installation's "bin"
directory and unzip the downloaded file which will produce either
caret5 or caret5.exe. You might have to change the permissions on
linux using the command "chmod a+rx caret5".
As for the negative "x" voxel size, this usually means the the origin
is specified on the right side of the volume and that the voxels are
ordered right-to-left. When Caret reads a volume and the volume
contains valid orientation information, Caret "flips" the volume in
memory to place the volume in an LPI (-x=left, -y=posterior, -
z=inferior) orientation. Visit the website "http://
www.grahamwideman.com/gw/brain/orientation/orientterms.htm" for more
information.
----------------------------------------------------------
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 15, 2006, at 4:08 AM, Mateus Joffily wrote:
Hi John,
Thank you very much. The image looks good to me. I use Linux and
Windows (preference for Linux).
Just one more question: How does Caret deals with the negative 'x'
voxel size set by SPM5? Does it affect the way Caret displays the
image? In the 'Volume Attributes Editor' dialog - 'Resample' tab,
the voxel size is always positive.
thanks,
Mateus
John Harwell wrote:
Hi Mateus,
I think I have the problem corrected and here is how
3D_original.nii appears in Caret. If the images look good to you
let me know which operating system you are using and I will make
an update available for you to download. This problem only
occurred if the X-axis was not left/right, the Y-axis was not
posterior/anterior, or the Z-axis not inferior/superior.
----------------------------------------------------------
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 13, 2006, at 3:33 AM, Mateus Joffily wrote:
Hi John,
I uploaded four files in Caret, their names are:
1) 3D_original.nii : original volume that doesn't display
correctly in Caret (case 1 described in my previous message)
2) 3D_original_spm5.pdf : capture of 3D_original.nii display in spm5
1) 3D_resliced.nii : same original volume but resliced (case 2
described in my previous message)
1) 3D_resliced_spm5.pdf : capture of 3D_resliced.nii display in spm5
Thank you very much.
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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