Mateus,
A volume has three-dimensions which are commonly indexed with I, J,
and K.
When Caret loads a volume it always stores the voxels such that the
voxels run left-to-right in the first dimension ("I"), posterior-to-
anterior in the second dimension ("J"), and inferior-to-superior
("K") in the third dimension. This is commonly referred to as an
"LPI" orientation and negative X points to the left side of the head,
negative Y points to the back of the head, and negative Z points down
into the neck. This is the same orientation used by the Talairach
atlas which places the origin at the anterior commissure.
Your volume has the voxels running anterior-to-posterior in the first
dimension ("I"), inferior-to-superior in the second dimension ("J"),
and left-to-right in the third dimension("K"). This is an AIL
orientation.
Since Caret wants the volume in an LPI orientation and your volume is
in an AIL orientation, Caret will reorganize the voxels in memory so
that the volume is in an LPI orientation. It is this reorientation
operation that results in the voxel sizes and dimensions being permuted.
Output of 3DInfo for your volume and your volume saved by Caret with
an LPI orientation:
Dataset File: 3D_original.nii
Identifier Code: NII_Oo8IAJJUzJFWVH2nBnBIQA Creation Date: Thu Nov
16 13:44:28 2006
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = MSB_FIRST]
Storage Mode: NIFTI file
Data Axes Orientation:
first (x) = Anterior-to-Posterior
second (y) = Inferior-to-Superior
third (z) = Left-to-Right [-orient AIL]
R-to-L extent: -80.652 [R] -to- 79.248 [L] -step- 1.300 mm
[124 voxels]
A-to-P extent: -73.912 [A] -to- 113.588 [P] -step- 0.938 mm
[201 voxels]
I-to-S extent: -70.210 [I] -to- 70.415 [S] -step- 0.938 mm
[151 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is float
-----------------
Dataset File: 3D_original_saved_with_caret.nii
Identifier Code: NII_Ffg_VXBk3o4b2q-dpSG84g Creation Date: Thu Nov
16 13:44:41 2006
Dataset Type: Anat Bucket (-abuc)
Byte Order: MSB_FIRST {assumed} [this CPU native = MSB_FIRST]
Storage Mode: NIFTI file
Data Axes Orientation:
first (x) = Left-to-Right
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient LPI]
R-to-L extent: -80.653 [R] -to- 79.248 [L] -step- 1.300 mm
[124 voxels]
A-to-P extent: -73.912 [A] -to- 113.588 [P] -step- 0.938 mm
[201 voxels]
I-to-S extent: -70.210 [I] -to- 70.415 [S] -step- 0.938 mm
[151 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is float
----------------------------------------------------------
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 16, 2006, at 11:39 AM, Mateus Joffily wrote:
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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