I want to add some to Xin's reply.<br><br><div class="gmail_quote">On Thu, Apr 5, 2012 at 2:55 PM, Peterson, Daniel <span dir="ltr"><<a href="mailto:petersond@kennedykrieger.org">petersond@kennedykrieger.org</a>></span> wrote:<br>
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<div>Hi All,</div>
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<div> I've got a couple of questions:</div>
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<div>1) What kind of re-orientation strategy does DTI Studio use when reorienting tensors for an LDDMM transformation of tensor data. Is there a reference available somewhere? As I understand, this is a non-trivial problem.</div>
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<div>2) What do the experts here feel about the feasibility of fiber-tracking in atlas-space? I know that this is traditionally considered undesireable, but do people think that perhaps with these more advanced methods, standard-space tractography could be
feasable?</div>
<div><br></div></div></div></blockquote><div>If you want to transfer tractography results to an atlas space, you have several options;</div><div>a) perform tractogrpahy in the native space, convert the trajectory information into a binary masking information, and transform the binary information into the atlas space. Repeat it for multiple subjects and create population data.</div>
<div>b) Transform the image into the atlas space and perform tractography. Repeat it for multiple subjects and create poulation data.</div><div>c) Transform the image in to the atlas space. Repeat it to for multiple subjects and create population-averaged tensor map. Then perform tractography.</div>
<div><br></div><div>#b and #c requires normalization of the tensor fields as described in your question #1. I think all approaches are valid.</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>3) Are there any command-line tools available for working with LDDMM transformations in a scriptable, automated manner? It would help our productivity immensely if we could apply Hmaps and Kimaps from the command-line, without clicking on buttons. Being
able to combine transformation matrices programmatically would be great as well.</div></div></div></blockquote><div><br></div><div>We have not been very enthusiastic about automated pipelines both for DtiStudio and MriStudio. This is because of quality control. We thought it is very important to check each step of image processing and this is the very reason we developed these programs, which are built for visual inspection. The heart of the problem is, it is very difficult to come up with quantitative QC report. We have been investing a lot of effort on the automated pipeline with a good QC report. So far, it has been difficult to get one which is as good as visual inspection. However, we are getting there. I hope we can provide a good automated and quantitative QC for DtiStudio this year and hopefully a first version for MriStudio. Then automation itself would be an easy task for us.</div>
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<div>Thanks so much,</div>
<div>-Dan</div>
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