<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Thank you very much for your detailed explanation</div><div>Primarily, I would like to master the first approach ( manual), how can I load multiple patients for registration and then slice by slice processing to do group analysis, is AIR program included within DTI studio, or is a separate program. Please can you tell me step by step like 1, 2, ..... </div><div><br></div><div>Thank you very much</div><div><br>On Feb 23, 2013, at 5:07 PM, "susumu mori" <<a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>> wrote:<br><br></div><blockquote type="cite"><div><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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?<br>
<br></blockquote><div><br></div><div>There are multiple approaches;</div><div><br></div><div>1) Manual approach in the native space:</div><div><br></div><div>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.</div>
<div><br></div><div>You can find some protocols in this paper;</div><div><span style="font-size:11.0pt;font-family:"Times New Roman","serif"">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</span></div><div><span style="font-size:11.0pt;font-family:"Times New Roman","serif""><br></span></div><div>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;</div>
<div><br></div><div><span style="font-size:11.0pt;font-family:"Times New Roman","serif"">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</span></div><div><br></div><div>2) Automated approach in the native or MNI space:</div><div><br></div><div>These papers describe automated ROI placements;</div><div><br></div><div><span style="font-size:11.0pt;font-family:"Times New Roman","serif"">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</span></div><div><span style="font-size:11.0pt;font-family:"Times New Roman","serif""><br></span></div><div><span style="font-size:11.0pt;font-family:"Times New Roman","serif"">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</span></div><div><span style="font-size:11.0pt;font-family:"Times New Roman","serif""><br></span></div><div>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.</div>
<div><br></div><div>3) Probabilistic approach:</div><div><br></div><div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div>These papers describe this approach;</div><div><br></div><div><span style="font-size:11.0pt;font-family:"Times New Roman","serif"">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</span></div><div><br></div><div><span style="font-family:'Times New Roman',serif;font-size:14.399999618530273px">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</span></div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
2. Can I load an anatomical sequence over DTI data eg. Color map or fA map etc...?<br>
<br></blockquote><div><br></div><div>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. </div>
<div><br></div><div>Please be careful because all MriStudio family programs use Radiology convention (right is left) while many other programs follow Neurology convention (right is right).</div><div><br></div><div>susumu</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks<br>
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