Hi John,
45 degrees was just to make it easier the visualization of how Caret deals
with the transformation matrix.
A more realistic example would be the transformation after coregistration.
If I coregister the 3D to the functional volumes, probably the 3D volume
will not be in one of the standard orientations anymore. If Caret opens
the volume as if there was no orientation specified, the coregistration
will be lost.
After your explanations, it seems to me that I always need to reslice my
volumes before openning it with Caret (except when i am sure that the
volume is already stored in the standard orientation). Correct?
thanks,
Mateus
>
> 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
>>>>>>>>>> _______________________________________________
>>>>>>>>>> caret-users mailing list
>>>>>>>>>> caret-users@brainvis.wustl.edu
>>>>>>>>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> caret-users mailing list
>>>>>>>>> caret-users@brainvis.wustl.edu
>>>>>>>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________ caret-users
>>>>>>> mailing list caret-users@brainvis.wustl.edu http://
>>>>>>> pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> caret-users mailing list
>>>>>> caret-users@brainvis.wustl.edu
>>>>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> caret-users mailing list
>>>>> caret-users@brainvis.wustl.edu
>>>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
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>>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>
>>>
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>>>
>>>
>>
>> <3D_original_rotated_spm5.pdf>
>> _______________________________________________
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>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>
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