[Mristudio-users] mristudio-users Digest, Vol 54, Issue 2

Thu Dec 30 17:44:34 EST 2010

Correct me if I misunderstand Jeff's question, but

FA is fractional anisotropy, which is rotation invariant in definition.

Thus,  after you choose "rotate gradients if applicable", it's reasonable to
only has very small difference.

Liang 

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jeff Sadino
Sent: Thursday, December 30, 2010 2:36 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] mristudio-users Digest, Vol 54, Issue 2

I have also been testing out rotations on our Siemens scanner using
DTIStudio 3.0.2.  Using 10 subjects (with average rotations of 15 degrees)
from the VB13 and VA25 software versions, I ran each one through the LDDMM
process.  I then went back and ran each one through again, but this time, I
ticked on the "rotate gradients if applicable" button.  When I compared the
final FA results for each region after LDDMM, there was an average percent
difference of only 0.199%.  This is my first time working with rotation
effects, but I would have assumed that a rotation of 15 degrees would have
caused a larger difference in the FA maps?  Should I be doing something
different?

Also, using our VB17 software, I took a DTI with 0 degrees rotation, and
then another with 28 degree rotation, and saw an average FA percent
difference of 3%.  Does this seem reasonable?

Thank you,

Jeff

On Wed, Dec 29, 2010 at 5:17 PM, Darren Gitelman
<d-gitelman at northwestern.edu> wrote:

Susumu

I have done some experiments with both unrotated and rotated DTI
scans. This is for Siemens data acquired using VB17 software (most
recent). In the unrotated case the data were acquired with no
rotations applied, while in the rotated case the data were angled by
about 33.8 deg yaw and 12 deg roll.

I have some observations and 3 questions.  The questions pertain to
flipping of various gradient directions and the use of the rotate
gradients if applicable button.

--- In the unrotated case the gradient directions reported by
DTIstudio were flipped in y and z vs. the default Siemens gradients.
Once the gradients reported by DTIstudio were multiplied by [1 -1 -1]
they were within 0.53 degrees of the default Siemens gradients.

Q1. > Is this flipping to be expected?

Q2. > If it is expected, isn't this a problem, because had I entered
my default Siemens gradient directions instead of extracting from
Dicom then the y and z directions would have been incorrect?

--- Since no angulation was applied to the gradients the results from
DTIstudio did not change whether or not I clicked "Rotate gradients if
applicable". This is as expected.

--- In the rotated case the gradients are again flipped in the y and z
directions. However, the results are not the same as multiplying the
gradient values by the rotation matrix (It appears this process is
more complex than I expected, but after working through it in nibabel:
see- http://mail.scipy.org/pipermail/nipy-devel/2010-September/004768.html,
I agree that DTIstudio is probably rotating the gradients correctly.
The last thing I noticed, however, is that the results are again the
same whether or not I click rotate gradients if applicable.

Q3. > It appears that for Siemens data (VB17) the gradient rotation is
applied whether or not one clicks rotate gradients if applicable. Is
this correct?

Thanks,
Darren

>
> ---------- Forwarded message ----------
> From: susumu mori <susumu at mri.jhu.edu>
> To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support"
<mristudio-users at mristudio.org>
> Date: Mon, 27 Dec 2010 20:32:31 -0500
> Subject: Re: [Mristudio-users] gradient directions
> Hi Darren and Jeff,
> What Jeff said is correct. DtiStudio provides some handy functions such as
extracting gradient information from DICOM/Mosaic and apply rotation based
on the oblique angles. However, these functions are activated by users and
it is users who have to find out what is the correct way to get a gradient
table.
> As I mentioned before, for self-defense, I recommend to perform a couple
of imaging with severe oblique angles. For us, it is difficult to comment
differences with third party programs (we don't have experience with them),
but following are some important points to know;
> 1) The generic gradient tables provided by manufacturers may need to be
modified for x/y/z permutation and +/- definition.
> 2) The gradient table extracted from DICOM files may be used as is, but
that may not be the case for old DICOM formats.
> 3) We should be always careful when we use oblique angles.
> 4) The gradient table extracted from Siemens DICOM  (Mosaic) could be
different from the generic table because it contains a small amount of
contributions from imaging gradient.
> 5) As Jeff mentioned, to see the effect of the table recalculation based
on the oblique-angles, you need to close the window and reopen the initial
data input window. There, it remembers the results of the previous gradient
table calculation.
> Our past experience says that the generic Siemens gradient table and the
one extracted from  Mosaic are very close. The difference is usually within
+/- definition and the small image gradient contribution. The table remains
unchanged regardless of oblique angles (within the difference due to small
image gradient contribution).
> Please don't hesitate to further discuss this issue because there could be
something we are missing.
> On Mon, Dec 27, 2010 at 5:44 PM, Jeff Sadino <jsadino.queens at gmail.com>
wrote:
>>
>> Hi Darren,
>> I also spent some time on this recently on our Siemens VB17 software.
DTIStudio does not rotate the gradients until after you click "OK" to
visualize your images.  So regardless of whether or not you select "rotate
gradients if applicable", the gradient table that you will see DTIStudio
pull will be identical.  To see the modified table, visualize your data,
then close that window, then when you load up your next subject, you will
see the rotated table.
>> As far as I can tell, DTIStudio pulls whatever is written in the DICOM
header, without any modifications, unless you tell it to.
>> In the DICOM header, there is a tag called ImageOrientationPatient.
DTIStudio uses this tag to "know" whether or not a rotation is necessary.
>> I'm not sure about those specific third party programs, but I think some
of them flip the y direction so that they are more compatible with FSL
>> Hope it helps,
>> Jeff
>>
>> On Sun, Dec 26, 2010 at 3:18 PM, Darren Gitelman
<d-gitelman at northwestern.edu> wrote:
>>>
>>> Hi
>>>
>>> I know the issue of gradient directions has been brought up many
>>> times, but I am struggling with what the correct gradient directions
>>> should be. It's not that I doubt dtistudio, but I am puzzled by why
>>> the gradients end up different depending on how one converts the dicom
>>> data. I have spent some time plotting the gradient directions on a
>>> unit sphere and this is what i found (see below). I also have some
>>> questions about how dtistudio "knows" whether or not to rotate the
>>> gradients.
>>>
>>> I am using Siemens data acquired on a scanner with b17 software.
>>>
>>> If I click "get gradient from dicom file header" the values entered by
>>> DTIstudio don't seem to change whether or not I also click rotate
>>> gradients if applicable.
>>>
>>> Is DTIstudio automatically rotating the gradients when it gets them
>>> from the Siemens header?
>>>
>>> Clearly these gradients are different than if I pasted in the default
>>> Siemens gradients. How does DTIstudio know whether or not the
>>> gradients need rotating when I click the OK button? Here is what I
>>> mean- let's say I get the gradients from the Dicom image and I save
>>> these in a text file. Now I try 2 different ways of importing the DTI
>>> data: 1) in one case I paste the default Siemens gradients and in the
>>> other 2) I paste the gradients I obtained from the Dicom image. If I
>>> click rotate gradients if applicable, will DTIstudio know to rotate
>>> the gradients in case 1 (default Siemens directions) but not in case 2
>>> (acquired from Dicom file)?
>>>
>>> Is there any way to get the final gradients that DTIstudio is applying
>>> to the data?
>>>
>>> The whole process of obtaining the gradients seems to be somewhat of a
>>> mystery (to me anyway) and it's hard to know what is correct (at least
>>> for Siemens data). I also notice that the gradients obtained from the
>>> Dicom file are not the same as the gradients one obtains when
>>> converting the data via either dcm2nii
>>> (http://www.cabiatl.com/mricro/mricron/dcm2nii.html) or via mriconvert
>>> (http://lcni.uoregon.edu/~jolinda/MRIConvert/). The gradients from
>>> these conversions are flipped by -1 in the y direction from dtistudio.
>>> (In fact the gradients from mriconvert are nearly the same as
>>> dtistudio after accounting for this y-flip, while the gradients form
>>> dcm2nii are off by 4-6 degrees rotation after accounting for the
>>> y-flip).
>>>
>>> Any advice about the gradient directions and how to be sure what is
>>> correct would be appreciated.
>>>
>>> Thanks,
>>> Darren
>>> --
>>> Darren Gitelman, MD
>>> 710 N. Lake Shore Dr., 1122
>>> Chicago, IL 60611
>>> Ph: (312) 908-8614
>>> Fax: (312) 908-5073
>>> _______________________________________________
>>> mristudio-users mailing list
>>> mristudio-users at mristudio.org
>>> http://lists.mristudio.org/mailman/listinfo/
>>> Unsubscribe, send a blank email to:
mristudio-users-unsubscribe at mristudio.org
>>
>>
>> _______________________________________________
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>
>
>
> ---------- Forwarded message ----------
> From: HUA KEGANG <khua1 at jhu.edu>
> To: mristudio-users at mristudio.org
> Date: Tue, 28 Dec 2010 16:45:35 +0000
> Subject: Re: [Mristudio-users] update of gradient table in DtiStudio
> Hi, Luca
>
> The MI algorithm optimizes the normalized mutual information.
>
> Thanks!
>
> KEGANG(LUKE) HUA
> Department of Radiology
> Johns Hopkins University School of Medicine
> 720 Rutland Ave Traylor217
> Baltimore, MD, 21205
>
>
>
>
>> Date: Mon, 27 Dec 2010 09:38:00 +0100
>> From: luca.binotto at unipd.it
>> Subject: [Mristudio-users] update of gradient table in DtiStudio
>> To: mristudio-users at mristudio.org
>>
>> Hello Susumu,
>>
>> I would like to know something about the way DtiStudio performs the
update
>> of the gradient table after the realignment of the dti dataset with
>> respect to the mean_b0 volume.
>>
>> The registration algorithm implemented in DtiStudio using mutual
>> information (MI):
>> 1) does it uses normalized mutual information or which other formulation
?
>> 2) how is the gradient table updated ? (rough simple theory)
>> After realignment of the DWI volumes, b-matrix (the gradient table) must
>> be updated.
>>
>> Patient motion and eddy currents can cause errors in the calculation of
>> parameters that describe diffusion in each voxel of a DWI dataset.
>> In normal conditions eddy currents contribution should be
>> very small (< 1% ?).
>> But the b-matrix (gradient table) is calculated with respect to a fixed
>> coordinate system (at the acquisition time) so the b-matrix must be
>> rotated accordingly to the transformation applied for image registration
>> otherwise we should get poor fiber statistics and some fibers possibly
>> deviate.
>>
>> So the gradient table is affected by rotations. Translations don't
>> change it.
>> But what does it happen with resampling (applying a scaling factor: es.
>> affine transformation) to a dwi dataset?
>> According to you is normally its effect small (as for eddy currents
>> effect) or can be more important?
>> For example a scaling factor such that a volume with a voxel size of
>> 2x2x2 mm3 is resliced to a 1x1x1 mm3 voxel size can be important its
>> effect or "only" a lower image quality (eg. I read somewhere of a
>> "red background" superimposed to the correct color map)?
>>
>>
>> thanks in advance,
>> best regards,
>>
>> Luca
>>
>>
>>
>>
>> _______________________________________________
>> mristudio-users mailing list
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mristudio-users-unsubscribe at mristudio.org
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/mristudio-users
>
>

--
Darren Gitelman, MD
710 N. Lake Shore Dr., 1122
Chicago, IL 60611
Ph: (312) 908-8614
Fax: (312) 908-5073

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