[Mristudio-users] DTI

[susumu mori]

> I would like to ask if  1. I can measure FA value, ADC or MD in a specific
> ROI or along a specified tract in order to have data in an objective way?
>
>
There are multiple approaches;

1) Manual approach in the native space:

You need to establish a protocol for manual placement of ROIs. After manual
fiber reconstruction, as Dorian pointed out, DtiStudio can report averaged
pixel intensities (e.g. FA, MD, etc) of the all pixels that contain the
fibers or report slice-by-slice numbers.

You can find some protocols in this paper;
Wakana S, Caprihan A, Panzenboeck MM, Fallon JH, Perry M, Gollub RL, Hua K,
Zhang J, Jiang H, Dubey P, Blitz A, van Zijl P, Mori S. Reproducibility of
quantitative tractography methods applied to cerebral white matter.
Neuroimage 2007;36(3):630-644, PMC2350213

When you use the slice-by-slice reports, instead of one value averaged over
an entire tract, you have to "register" data from different subjects
because, say, an averaged FA of a tract at "axial slice#10" of one subject
may not be the same anatomical slice of "axial slice#10" of the other
subject. An example of this operation can be found in this paper;

Stieltjes B, Kaufmann WE, van Zijl PC, Fredericksen K, Pearlson GD,
Solaiyappan M, Mori S. Diffusion tensor imaging and axonal tracking in the
human brainstem. Neuroimage 2001;14(3):723-735

2) Automated approach in the native or MNI space:

These papers describe automated ROI placements;

Zhang W, Olivi A, Hertig SJ, van Zijl P, Mori S. Automated fiber tracking
of human brain white matter using diffusion tensor imaging. Neuroimage
2008;42(2):771-777, PMC2585359

Zhang Y, Zhang J, Oishi K, Faria AV, Jiang H, Li X, Akhter K, Rosa-Neto P,
Pike GB, Evans A, Toga AW, Woods R, Mazziotta JC, Miller MI, van Zijl PC,
Mori S. Atlas-guided tract reconstruction for automated and comprehensive
examination of the white matter anatomy. Neuroimage 2010;52(4):1289-1301,
PMC2910162

The idea is, you can define ROIs (or use our pre-defined brain parcellation
maps) once in an MNI atlas and warp these ROIs to each subject for
automated tracking. Yajing Zhang has many pre-defined ROI sets in our brain
parcellation maps. I believe you can download them from our websites.

3) Probabilistic approach:

One issue of #1 and #2 approaches is that the streamline generation has a
large amount of variability. Another common issue is, if there are lesions
with low FA, tractography is influenced by that. Our atlases have
probabilistic tract locations. For example, we have reconstructed the
corticospinal tracts in normal subjects and the results are registered into
the MNI space, creating probabilistic map of the corticospinal tract in the
MNI space. If you normalize your patient brains to the MNI space, you can
superimpose these probabilistic maps on the patient brains and quantify
averaged pixel intensities.

There are pre-defined probabilistic maps of many tracts in RoiEditor, which
can be applied for automated pixel intensity calculation of various white
matter tracts. Downside of this approach is, it assumes that tract
locations of your patient population are not significantly altered and
therefore after normalization to the MNI space, the probabilistic maps can
accurately define the properties of each tract of interest.

These papers describe this approach;

Hua K, Zhang J, Wakana S, Jiang H, Li X, Reich DS, Calabresi PA, Pekar JJ,
van Zijl PC, Mori S. Tract probability maps in stereotaxic spaces: analyses
of white matter anatomy and tract-specific quantification. Neuroimage
2008;39(1):336-347, PMC2724595

Zhang Y, Zhang J, Oishi K, Faria AV, Jiang H, Li X, Akhter K, Rosa-Neto P,
Pike GB, Evans A, Toga AW, Woods R, Mazziotta JC, Miller MI, van Zijl PC,
Mori S. Atlas-guided tract reconstruction for automated and comprehensive
examination of the white matter anatomy. Neuroimage 2010;52(4):1289-1301,
PMC2910162


> 2. Can I load an anatomical sequence over DTI data eg. Color map or fA map
> etc...?
>
>
Of course, you first have to register your anatomical image (like T1) to
your DTI (or register DTI to T1). Then you can load both T1 and DTI to
RoiEditor. We don't have image-to-image overlay functions with transparency
control. You have to define "object (ROI)" using one of the image (like
tract locations from DTI or thresholded high FA regions) and then
superimpose the object (ROI) to the other image (like T1). In RoiEditor,
the tract streamline information have to be converted to 3D image format
(like a masking file in which pixels that contain a fiber are "1" and all
other are "0", or each pixel contains a probabilistic value). If you load
the co-registered T1 to DtiStudio, you can superimpose streamline
information on T1. For T1-DTI co-registration, you can use our DiffeoMap or
other software like FSL and SPM.

Please be careful because all MriStudio family programs use Radiology
convention (right is left) while many other programs follow Neurology
convention (right is right).

susumu


> Thanks
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