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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Shan,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hangyi may have a more “official”
answer to your question, but I want to introduce you to the “Binary Map”
option.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>When you store your ROI, there are several
options for the format and one of them is the “Binary Map”. If you
click it, you get 3 files. Two 3D binary files (your ROI pixels are 1 and all
other pixels are 0) and one text file. You get the two binary files because you
drew 2 ROIs. If you drew 3 ROIs, you get 3 binary files. Please open the text
file and study what’s inside. It is like a header file containing
information about the ROI binary file paths and image dimensions. There you can
also find “operation” fields, in which you can specify how to use
each ROI files. If one ROI have operation “0”, then it is used as “OR”.
“1” is for “AND”. There is an explanation at the end of
the file. You can specify the two ROI files for CUT#1 and CUT#2 too. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>This format is much more powerful because
you can import any 1/0 binary maps, such as fMRI activation maps, and combine
them with different operators (OR, AND, NOT, CUT etc). Also in this way, you
should not have the problem you reported.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Susumu<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 color=black face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma;color:windowtext;font-weight:bold'>From:</span></font></b><font
size=2 color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:windowtext'> mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b><span style='font-weight:
bold'>On Behalf Of </span></b>Shan.Shen@surrey.ac.uk<br>
<b><span style='font-weight:bold'>Sent:</span></b> Thursday, August 28, 2008
6:32 AM<br>
<b><span style='font-weight:bold'>To:</span></b> mristudio-users@mristudio.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [Mristudio-users] Save
ROIs in fibre tracking</span></font><font color=black face="Times New Roman"><span
style='font-family:"Times New Roman";color:windowtext'><o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 color=black face="sans serif"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman"'>Hi,</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman"'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman"'>I would like
to use the ‘cut’ operation to track fibres between two ROIs. I did
the fibre tracking first, then drew the two ROIs, the fibres displayed were
those between the two ROIs. However, if I save the ROIs and load them again,
this time the fibres displayed are not the ones between the ROIs anymore, but
are fibres passing through one of the ROIs. Could anyone tell me what the
possible problem is? I tried saving the ROIs as different formats, but the
problem is the same.</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman"'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman"'>Many thanks</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman"'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman"'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman"'>shan </span></font><o:p></o:p></p>
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