[Mristudio-users] Fwd: loading DSI dataset into DTIStudio
Xin Li
xli16 at jhmi.edu
Mon Mar 18 08:31:31 EDT 2013
1) We are first time users of LDDMM and and are encountering a problem when we use the single channel registration: "file not found: process.md5".
Is DiffeoMap on a network disk instead of on your local disk?
Xin
----- Original Message -----
From: Usha Sinha <usinha at mail.sdsu.edu>
Date: Sunday, March 17, 2013 3:52 pm
Subject: Re: [Mristudio-users] Fwd: loading DSI dataset into DTIStudio
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>, susumu at mri.jhu.edu
Cc: Vadim Malis <vadmalis at gmail.com>
> Hi Susumu
> I apologize for using your direct mail but I had some problems
> logging into
> the forum.
> I have the following questions:
>
>
> *LDDMM*
>
> 1) We are first time users of LDDMM and and are encountering a problem
> when we use the single channel registration: "file not found:
> process.md5". Further, we are using the LDDMM to correct for distortions
> in muscle DTI images, these images are acquired rather anisotropically
> (1.4mm in plane and 5 mm thickness), so the requirement for isotropic
> voxel
> in LDDMM is a stretch. Is there a LDDMM algorithm as a 2D version
> available where we correct on slice by slice basis as the maximum
> distortions are along the in-plane phase encode. Our T2 and b0
> slices are
> matched acquisitions. If a 2D version is not available, would it be
> OK to
> reslice the T2 and DTI volumes to be isotropic despite a highly anisotropic
> acquisition?
> *Fiber Tracking*
>
> 1) When performing tracking in DTIStudio, is there a way to obtain a
> track
> through a selected voxel. The reason I ask is that when selecting
> even a
> single voxel ROI, the number of tracks through it more than one; this
> is
> from the brute force aspect of the algorithm, I guess. We are trying
> to
> get muscle fiber pennation angles using seed points starting near the
> aponeurosis. It will help us in trying to get the fiber that originates
> from the seed point rather than the ROI at that seed point (or is
> there a
> non-brute force available).
>
> 2) This feature (getting the fiber coordinates from a seed voxel) is
> also
> important for our brain fiber atlases where we are trying to evaluate
> the
> quality of tracking in atlases generated by different methods. One method
> suggested is the sum of distances of equally spaced points along the
> fiber
> tract starting from the seed point in atlas and subjects. The other method
> to compare is the track end point divergence. When several tracks go
> through a single voxel ROI, it makes comparisons difficult.
>
>
> Thanks
>
> Usha
>
>
>
>
>
> On Fri, Mar 15, 2013 at 4:27 PM, susumu mori <susumu at mri.jhu.edu> wrote:
>
> > OK, Deepa,
> >
> > I believe you did a typical DSI study. Because it would be of
> interest for
> > many DtiStudio users, allow me to share my response to you,
> together with
> > your images.
> >
> > There are two important differences between DTI and DSI.
> > First, of course, DSI requires many more gradient orientations. In
> your
> > case, you used 257 directions. In general, 100 orientation measurement
> > takes more than 10 min. So, 257 orientations would take about 30
> min. You
> > repeated it twice. So, it must take 1 hour, if I'm not mistaken.
> > I once asked Van Wedeen about how many orientations would be preferable.
> > He said, "even 300 is very sparse, if you map them on the surface
> of a
> > sphere. So, the more the better" was his reply.
> > On the other hand, if you use a model like spherical decomvolution,
> there
> > are papers demonstrating directions as few as 60 would give you decent
> > estimation of crossing fibers. I don't have an answer to it.
> >
> > Second, high-angular resolution imaging like DSI requires higher b
> > values. This actually have more profound effects on your experiment
> design
> > and image quality. DTI typically uses b = 700-1,000. The higher you
> go, the
> > more signal you loose, more motion artifacts you get, and more eddy
> current
> > distortion you suffer. On top of it, because each image is so noisy,
> > detection and correction of artifacts become more difficult. DSI
> requires b
> > = 3,000 - 30,000, which is much higher than DTI.
> >
> > Some people believe DSI data naturally includes DTI data.
> Therefore, once
> > you get DSI data, you wouldn't loose anything. However, that is not
> the
> > case, because you suffer from SNR loss and more artifacts. This is
> why it
> > is difficult to adopt DSI protocols for routine research and clinical
> > studies.
> >
> > I attached a nice paper by Derek discussing this issue.
> >
> > Now, let's go back to your images. The b0 looks good. The DWIs are
> what
> > you would expect from high b-value DWIs. Your images look very
> similar to
> > Fig. 3 in Derek's paper with b=2,000-3,000. So your data are fine.
> They
> > don't look like typical DTI data because I bet that the b-values
> you used
> > are b = 2,000-3,000.
> >
> > You have slight ghosting in the background, but it seems
> calibration error
> > for your EPI phase correction; not a major problem, I think.
> >
> > So, the bottom line is, your DICOM files were correctly read. The
> > appearance of DWIs should be different between DSI and DTI
> protocols and
> > your images are what you expect.
> >
> > Hope this will help.
> >
> > Susumu
> >
> > On Fri, Mar 15, 2013 at 6:31 PM, Deepa Krishnaswamy <
> > deepa.krishnaswamy1 at gmail.com> wrote:
> >
> >> Hi,
> >> I have attached a power point with a few images.
> >> Yes I did read the data as Mosaic. There are 515 gradient
> directions in
> >> total, which is comprised of repeated 257 directions plus 1 b0.
> >> I do know that DTIStudio does not support DSI data analysis, but
> isn't it
> >> still possible to fit the DTI model to DSI data?
> >> I also just wanted to run through the LDDMM pipeline to get our data
> >> registered to the same space as the JHU MNI WM atlas, and then use
> our own
> >> tractography algorithms.
> >> I hope this is possible, thanks.
> >>
> >> Deepa
> >>
> >> On Thu, Mar 14, 2013 at 10:20 AM, susumu mori <susumu at mri.jhu.edu>
> wrote:
> >>
> >>> Hi Deepa,
> >>>
> >>> Did you read the data as Mosaic?
> >>> Please send me the actual images in PowerPoint.
> >>>
> >>> If you are using non off-the-shelf image protocol, it is possible
> that
> >>> DtiStudio can't read the user-defined data format.
> >>> If you get a custom data acquisition method from somebody, I encourage
> >>> you to talk with them about how to read the data. DtiStudio
> doesn't support
> >>> DSI data analysis anyway.
> >>>
> >>> Susumu
> >>>
> >>> On Tue, Mar 12, 2013 at 9:50 PM, Deepa Krishnaswamy <
> >>> deepa.krishnaswamy1 at gmail.com> wrote:
> >>>
> >>>> Hi,
> >>>> I have a DSI dataset in MOSAIC format, along with the
> corresponding b
> >>>> btable. I noticed that after loading in the data, some of it appears
> >>>> extremely blurry/shifted. I know that the data actually does not
> look like
> >>>> this, as I have used other programs to view the raw data. Has
> anybody else
> >>>> encountered this problem?
> >>>> Thanks,
> >>>>
> >>>> Deepa
> >>>>
> >>>> _______________________________________________
> >>>> mristudio-users mailing list
> >>>> mristudio-users at mristudio.org
> >>>>
> >>>> Unsubscribe, send a blank email to:
> >>>> mristudio-users-unsubscribe at mristudio.org
> >>>>
> >>>>
> >>>
> >>
> >
> > _______________________________________________
> > mristudio-users mailing list
> > mristudio-users at mristudio.org
> >
> > Unsubscribe, send a blank email to:
> > mristudio-users-unsubscribe at mristudio.org
> >
> >
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
>
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20130318/0011e2b0/attachment.html
More information about the mristudio-users
mailing list