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<BODY lang=EN-US vLink=purple link=blue><![if !supportLists]>
<DIV dir=ltr align=left><SPAN style="mso-list: Ignore">1.<SPAN
style="FONT: 7pt 'Times New Roman'">
</SPAN></SPAN><![endif]>How do I select a portion of a selected fiber in DTI
studio? <SPAN class=792381920-19012009><FONT face=Arial color=#0000ff
size=2> </FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=792381920-19012009></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT face=Arial
color=#0000ff size=2>> Use the Cut operation. </FONT> <FONT face=Arial
color=#0000ff size=2>After you click CUT, it waits for two inputs. The first ROI
will be treated as "OR" and the result looks like "OR". Proceed for the second
ROI. After the input of the second ROI, only the projection between the two ROIs
are constructed.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT face=Arial
color=#0000ff size=2>> Use the "Statistics -> Profile" function. If the
trajectory of the reconstructed fiber is rather straight (not U-shape), you can
use this function. It generates a table in which you can see pixel values
averaged over axial, coronal, and sagittal slices. In this way, you can retrieve
values at each slice level.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT face=Arial
color=#0000ff size=2>> Use RoiEditor: Save the result as a "binary" format
and read it to RoiEditor together with the image you want to quantify (e.g. FA
map). With some creative mind, you can do several interesting things using
functions in RoiEditor.<![if !supportLists]> For example, with a region growing
tool, you can re-define the fiber coordinates within RoiEditor (called
"object") and apply it as an ROI to any co-registered images such as
FA. You can manually modify the object. You can also manually remove the fiber
coordinate in the binary map at one slice level. Then you can do region growing
to define a new object and the region growing will stop at the slice level you
modified.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN style="mso-list: Ignore"><SPAN
class=792381920-19012009><FONT face=Arial color=#0000ff
size=2> </FONT></SPAN></SPAN></DIV>
<DIV dir=ltr align=left><SPAN style="mso-list: Ignore"><SPAN
class=792381920-19012009> </SPAN>2.<SPAN
style="FONT: 7pt 'Times New Roman'"> </SPAN><![endif]></SPAN>How do I modify the fiber-data file within DTI studio or
using other softwares such as MATLAB?<SPAN class=792381920-19012009><FONT
color=#0000ff size=2> </FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT color=#0000ff
size=2>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT face=Arial
color=#0000ff size=2>> In the FAQ section of <A
href="http://www.mristudio.org">www.mristudio.org</A>, there is a section
explaining the format of the DtiStudio fiber files. If you saved your fiber in
this format, you can reload and re-edit them in DtiStudio. Once you convert the
data into the binary format (1/0 for each pixel), RoiEditor is the way to go to
modify them. </FONT></SPAN></DIV></FONT></SPAN></DIV>
<DIV class=Section1>
<P class=MsoListParagraph
style="TEXT-INDENT: -0.25in; mso-list: l0 level1 lfo1"><SPAN
class=792381920-19012009> </SPAN><o:p></o:p></P><![if !supportLists]>
<P class=MsoListParagraph
style="TEXT-INDENT: -0.25in; mso-list: l0 level1 lfo1"><SPAN
style="mso-list: Ignore">3.<SPAN
style="FONT: 7pt 'Times New Roman'">
</SPAN></SPAN><![endif]>How can I read fiber-tracking results saved in Analyze
format back into DTI studio (it only seems to work for dat format)?<FONT
color=#0000ff><FONT size=2><SPAN
class=792381920-19012009> </SPAN></FONT></FONT></P>
<P class=MsoListParagraph
style="TEXT-INDENT: -0.25in; mso-list: l0 level1 lfo1"><FONT color=#0000ff><FONT
size=2><SPAN class=792381920-19012009> </SPAN><SPAN
class=792381920-19012009> </SPAN></FONT></FONT></P><SPAN
class=792381920-19012009>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT face=Arial
color=#0000ff size=2>> If I'm not mistaken, fiber-tracking results in Analyze
format is pixel-by-pixel "image data" (for example, 256x256x50 matrix data). For
example, a binary image in which pixels that contain the fiber is 1 and
everything else is 0. The original "loss-less" fiber-tracking file should
be streamline information, not the pixel-by-pixel information. For exmaple, such
file should contain information about how many fibers are reconstructed and then
coordinate information of each line. Once this type of streamline information is
converted to an image format, the tracking information is degenerated and
streamline can not be reconstructed (and further editing is impossible). So,
yes, you need the dat format to prevent any information
loss.</FONT></SPAN></DIV></SPAN>
<P class=MsoListParagraph
style="TEXT-INDENT: -0.25in; mso-list: l0 level1 lfo1"><SPAN
class=792381920-19012009> </SPAN><o:p></o:p></P><![if !supportLists]>
<P class=MsoListParagraph
style="TEXT-INDENT: -0.25in; mso-list: l0 level1 lfo1"><SPAN
style="mso-list: Ignore">4.<SPAN
style="FONT: 7pt 'Times New Roman'">
</SPAN></SPAN><![endif]>Where can I access information such as #fibers for a
particular voxel?<SPAN class=792381920-19012009><FONT color=#0000ff
size=2> </FONT></SPAN></P>
<P class=MsoListParagraph
style="TEXT-INDENT: -0.25in; mso-list: l0 level1 lfo1"><SPAN
class=792381920-19012009><FONT color=#0000ff
size=2></FONT></SPAN> </P><SPAN class=792381920-19012009>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT face=Arial
color=#0000ff size=2>> That's a good question</FONT><FONT face=Arial
color=#0000ff size=2>. I believe that there is a version that can save an image
for "the number of fibers at each pixel". </FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT face=Arial
color=#0000ff size=2>> Hangyi, the version with this function is
ready?</FONT></SPAN></DIV></SPAN>
<P class=MsoListParagraph
style="TEXT-INDENT: -0.25in; mso-list: l0 level1 lfo1"><SPAN
class=792381920-19012009> </SPAN><o:p></o:p></P><![if !supportLists]>
<P class=MsoListParagraph
style="TEXT-INDENT: -0.25in; mso-list: l0 level1 lfo1"><SPAN
style="mso-list: Ignore">5.<SPAN
style="FONT: 7pt 'Times New Roman'">
</SPAN></SPAN><![endif]>Are the statistical calculations given by the Statistics
Profile weighted by fibers/voxel?<SPAN class=792381920-19012009><FONT
color=#0000ff size=2> </FONT></SPAN></P>
<P class=MsoListParagraph
style="TEXT-INDENT: -0.25in; mso-list: l0 level1 lfo1"><SPAN
class=792381920-19012009></SPAN> </P><SPAN class=792381920-19012009>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT face=Arial
color=#0000ff size=2>> Yes, the current version is weighted by the
fibers/voxel, but we have a newer version in which you can choose weighting /
not weighting.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=792381920-19012009></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=792381920-19012009><FONT face=Arial><FONT
color=#0000ff size=2>> I'll check the status of the latest version. I think
we will release Version 3, non-beta very soon.</FONT></FONT></SPAN></DIV>
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style="TEXT-INDENT: -0.25in; mso-list: l0 level1 lfo1"> </SPAN><o:p></o:p></P></DIV></BODY></HTML>