On Nov 17, 2006, at 12:38 PM, Mateus Joffily wrote:
Hi John,
Thanks. Now, I understand. I thought that the reported dimensions
and voxel sizes refered to the volume (I,J,K) dimensions (voxel
coordinates), and not to the (X,Y,Z) dimensions (real world
coordinates). Please, correct me if I am still wrong?
You might call it real world coordinates but I would probably call it
stereotaxic coordinates.
I have another question: Does Caret take into account any rotation
specified in the nifti-1 header? Or is there any incompatibility
with transformations done by SPM5?
To better explain my question, let me describe the following test
that I did:
1) I rotated my 3D_original.nii image of 45degrees around the X-
axis (see 3D_original_rotated_spm5.pdf).
2) I saved this rotation in the image header, but I didn't reslice
the image.
3) When I loaded the rotated image with Caret, I couldn't see
anything in the P(YZ) and C(XZ) planes. However the H(XY) plane was
displayed as if the image was not rotated. When I used the 'x', 'y'
and 'z' control buttons to navigate through the image, the H(XY)
slices were displayed as if it was the non-rotated 3D_original.nii.
The reported dimensions and voxel sizes were 124x201x151 and
1.3x1.326x0.00, respectively.
Is it right?
Why would you store a volume at a 45 degree orientation?
When Caret reads a NIFTI volume, it examines the transformation
matrix to determine the orientation of the volume's three axes. If
these orientations correspond what I would call the standard
orientations (left-to-right, right-to-left, anterior-to-posterior,
posterior-to-anterior, inferior-to-superior, or superior-to-
inferior), Caret will permute the volume so that it is displayed
properly. If the orientations of the axes do not correspond to the
standard orientations, Caret will read the volume and display the
volume as if there was no orientation data in the volume.
Thanks,
Mateus
John Harwell wrote:
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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<3D_original_rotated_spm5.pdf>
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