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

Thu Dec 30 17:36:24 EST 2010

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
> >>
> >>
> >> _______________________________________________
> >> mristudio-users mailing list
> >> mristudio-users at mristudio.org
> >> http://lists.mristudio.org/mailman/listinfo/
> >> Unsubscribe, send a blank email to:
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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
> >> mristudio-users at mristudio.org
> >> http://lists.mristudio.org/mailman/listinfo/
> >> Unsubscribe, send a blank email to:
> 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
>
> _______________________________________________
> 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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