Re: [caret-users] nifti images
Mateus,
My understanding is that most people register their volumes to one of
the standard stereotaxic spaces (AFNI Talairach, SPM, etc) during the
processing of their data. All of these standard stereotaxic spaces
have what I would call "orthogonal" or standard orientations (left-to-
right, posterior-to-anterior, etc.) so Caret is able to properly read
and display the volumes.
For Caret to properly display your volumes, you may need to reslice
them so that the data is stored along the "standard orientations".
John
On Nov 20, 2006, at 7:24 PM, [EMAIL PROTECTED] wrote:
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-t
Re: [caret-users] nifti images
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 C
Re: [caret-users] nifti images
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. Loui
Re: [caret-users] nifti images
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?
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?
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 an
Re: [caret-users] nifti images
Hi Mateus, I think it's worth trying to segment both volumes using Caret to see if there is a noticeable effect on surface quality. My guess is not much, but let us know if I'm wrong. Just make sure you resample to cubic 1mm (preferrably using some scriptable utility as part of a preprocessing script that may also include bias correction, if needed). On 11/16/2006 11:07 AM, Mateus Joffily wrote: Hi Donna, Usually, I also use SPM for resampling my images. When I resampled the 3D_resliced.nii image with SPM, the histogram showed the same spiking as the original image (3D_original.nii). Only when I resliced the image with Caret, the histogram got smooth. I don't know exactly why... To test the effects of the histogram bin on the final histogram distribution, I wrote a small matlab program (see attachment). As you can see, depending on the bin size, we can have a spiky histogram (top) or a smooth histogram (bottom). Both histograms were calculated from the same 3D_resliced.nii image. The spikes occur at bin intervals that encloses two successive integer intensity values. In my understanding, those spikes should happen whenever we have a discrete data set and non-integer bin size. What do you think? Thanks, Mateus Donna Dierker wrote: Hi Mateus, See inline replies below. On 11/14/2006 09:45 AM, Mateus Joffily wrote: Hi Donna, Thanks for your help. I am sending you two histograms of 3D_resliced.nii: (1) histogram_resliced_1.jpg is the same histogram you already sent to me; (2) histogram_resliced_2.jpg is the histogram of 3D_resliced.nii after resampling at 1x1x1mm with Caret. We can see that the spikes disapear in (2). It looks like much closer to the histograms described in your 'Peak Tweaking' document. As I don't have much experience with image segmentation, I was wondering if there was any problem with my images. I am glad to know that they look fine for you. Try segmenting both inputs using Caret and compare the results. You don't have to patch the resulting hemispheres to get a good feel for the quality; just looking at the fiducial surfaces and segmentations is generally adequate for judging which input is better, and if the differences matter. An unacceptably blurred structural MRI will have a smooth histogram, but probably won't produce a good segmentation. In both histograms, I could detect peaks, so there's probably adequate GM/WM contrast to get a good segmentation. May be the problem is the one pointed by Simon. If this is the case, adjusting the histogram bins could minimize the effect. Do we have control over the histogram bins with Caret interface? It doesn't look like it; the only inputs are the voxdims. To be honest, I rarely use Caret to resample my volumes. I usually do this as part of a preprocessing protocol using AFNI, FSL, or SPM utilities. They allow one to specify interpolation mode, etc. (At wustl.edu, this is done when the volume is written to 711-2B space using Avi Snyder's imgreg and related utilities.) Thanks, Mateus Dierker wrote: 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 app
Re: [caret-users] nifti images
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
Re: [caret-users] nifti images
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
Re: [caret-users] nifti images
Hi Donna, Usually, I also use SPM for resampling my images. When I resampled the 3D_resliced.nii image with SPM, the histogram showed the same spiking as the original image (3D_original.nii). Only when I resliced the image with Caret, the histogram got smooth. I don't know exactly why... To test the effects of the histogram bin on the final histogram distribution, I wrote a small matlab program (see attachment). As you can see, depending on the bin size, we can have a spiky histogram (top) or a smooth histogram (bottom). Both histograms were calculated from the same 3D_resliced.nii image. The spikes occur at bin intervals that encloses two successive integer intensity values. In my understanding, those spikes should happen whenever we have a discrete data set and non-integer bin size. What do you think? Thanks, Mateus Donna Dierker wrote: Hi Mateus, See inline replies below. On 11/14/2006 09:45 AM, Mateus Joffily wrote: Hi Donna, Thanks for your help. I am sending you two histograms of 3D_resliced.nii: (1) histogram_resliced_1.jpg is the same histogram you already sent to me; (2) histogram_resliced_2.jpg is the histogram of 3D_resliced.nii after resampling at 1x1x1mm with Caret. We can see that the spikes disapear in (2). It looks like much closer to the histograms described in your 'Peak Tweaking' document. As I don't have much experience with image segmentation, I was wondering if there was any problem with my images. I am glad to know that they look fine for you. Try segmenting both inputs using Caret and compare the results. You don't have to patch the resulting hemispheres to get a good feel for the quality; just looking at the fiducial surfaces and segmentations is generally adequate for judging which input is better, and if the differences matter. An unacceptably blurred structural MRI will have a smooth histogram, but probably won't produce a good segmentation. In both histograms, I could detect peaks, so there's probably adequate GM/WM contrast to get a good segmentation. May be the problem is the one pointed by Simon. If this is the case, adjusting the histogram bins could minimize the effect. Do we have control over the histogram bins with Caret interface? It doesn't look like it; the only inputs are the voxdims. To be honest, I rarely use Caret to resample my volumes. I usually do this as part of a preprocessing protocol using AFNI, FSL, or SPM utilities. They allow one to specify interpolation mode, etc. (At wustl.edu, this is done when the volume is written to 711-2B space using Avi Snyder's imgreg and related utilities.) Thanks, Mateus Dierker wrote: 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
Re: [caret-users] nifti images
Hi Mateus, See inline replies below. On 11/14/2006 09:45 AM, Mateus Joffily wrote: Hi Donna, Thanks for your help. I am sending you two histograms of 3D_resliced.nii: (1) histogram_resliced_1.jpg is the same histogram you already sent to me; (2) histogram_resliced_2.jpg is the histogram of 3D_resliced.nii after resampling at 1x1x1mm with Caret. We can see that the spikes disapear in (2). It looks like much closer to the histograms described in your 'Peak Tweaking' document. As I don't have much experience with image segmentation, I was wondering if there was any problem with my images. I am glad to know that they look fine for you. Try segmenting both inputs using Caret and compare the results. You don't have to patch the resulting hemispheres to get a good feel for the quality; just looking at the fiducial surfaces and segmentations is generally adequate for judging which input is better, and if the differences matter. An unacceptably blurred structural MRI will have a smooth histogram, but probably won't produce a good segmentation. In both histograms, I could detect peaks, so there's probably adequate GM/WM contrast to get a good segmentation. May be the problem is the one pointed by Simon. If this is the case, adjusting the histogram bins could minimize the effect. Do we have control over the histogram bins with Caret interface? It doesn't look like it; the only inputs are the voxdims. To be honest, I rarely use Caret to resample my volumes. I usually do this as part of a preprocessing protocol using AFNI, FSL, or SPM utilities. They allow one to specify interpolation mode, etc. (At wustl.edu, this is done when the volume is written to 711-2B space using Avi Snyder's imgreg and related utilities.) Thanks, Mateus Dierker wrote: 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 ___ 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 -
Re: [caret-users] nifti images
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 ___ ca
Re: [caret-users] nifti images
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
Re: [caret-users] nifti images
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
Re: [caret-users] nifti images
Hi Donna, Thanks for your help. I am sending you two histograms of 3D_resliced.nii: (1) histogram_resliced_1.jpg is the same histogram you already sent to me; (2) histogram_resliced_2.jpg is the histogram of 3D_resliced.nii after resampling at 1x1x1mm with Caret. We can see that the spikes disapear in (2). It looks like much closer to the histograms described in your 'Peak Tweaking' document. As I don't have much experience with image segmentation, I was wondering if there was any problem with my images. I am glad to know that they look fine for you. May be the problem is the one pointed by Simon. If this is the case, adjusting the histogram bins could minimize the effect. Do we have control over the histogram bins with Caret interface? Thanks, Mateus Dierker wrote: 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 ___ 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 <><>
Re: [caret-users] nifti images
Spikes in histograms like these can sometimes arise from quantization noise due to taking integer valued intensities and dividing into an integer number of bins. See for example this paper: http://www.ion.ucl.ac.uk/nmrphysics/paultofts/pdfs/B151_spikes_2003.pdf -- Simon Donna Dierker wrote: 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 ___ 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 -- Simon K. Warfield, Ph.D.[EMAIL PROTECTED] Phone: 617-732-7090 FAX: 617-582-6033 Associate Professor of Radiology, Harvard Medical School Director, Computational Radiology Laboratory, Departments of Radiology at Children's Hospital and Brigham and Women's Hospital, Thorn 329, Dept Radiology, Brigham and Women's Hospital 75 Francis St, Boston, MA, 02115 MA 280, Dept Radiology, Children's Hospital Phone: 617-355-4566
Re: [caret-users] nifti images
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 ___ 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 -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) <><>
Re: [caret-users] nifti images
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 ___ 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
Re: [caret-users] nifti images
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
