<div dir="ltr">I found that I can easily make mistake in the BinaryMap text file.<div>Start from just one ROI to get yourself familiarized. </div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Aug 7, 2013 at 11:40 AM, Dorian P. <span dir="ltr"><<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Try adding FiberColor and ColorMode. Also make sure the sizes of the image correspond. Below is an example that works for me.<div>
<br></div><div><br><div><div class="im"><div>*** ROI Map ***</div><div><br></div><div>Begin</div>
</div><div><span style="white-space:pre-wrap"> </span>ImageWidth:<span style="white-space:pre-wrap"> </span>181</div><div><span style="white-space:pre-wrap"> </span>ImageHeight:<span style="white-space:pre-wrap"> </span>217</div>
<div><span style="white-space:pre-wrap"> </span>ImageSlices:<span style="white-space:pre-wrap"> </span>181</div><div class="im"><div><br></div><div><span style="white-space:pre-wrap"> </span>PixelSizeWidth:<span style="white-space:pre-wrap"> </span>1.000000</div>
<div><span style="white-space:pre-wrap"> </span>PixelSizeHeight:<span style="white-space:pre-wrap"> </span>1.000000</div><div><span style="white-space:pre-wrap"> </span>SliceThickness:<span style="white-space:pre-wrap"> </span>1.000000</div>
<div><br></div><div><span style="white-space:pre-wrap"> </span>SliceOrientation:<span style="white-space:pre-wrap"> </span>1</div><div><span style="white-space:pre-wrap"> </span>SliceSequencing:<span style="white-space:pre-wrap"> </span>0</div>
<div><br></div></div><div><div> BinaryFile:<span style="white-space:pre-wrap"> </span>C:\temp\OR.dat</div><div><span style="white-space:pre-wrap"> </span>Operation:<span style="white-space:pre-wrap"> </span>0</div>
<div><span style="white-space:pre-wrap"> </span>FiberColor:<span style="white-space:pre-wrap"> </span>(255,0,0)</div><div><span style="white-space:pre-wrap"> </span>ColorMode:<span style="white-space:pre-wrap"> </span>0</div>
<div> <span style="white-space:pre-wrap"> </span></div><div> BinaryFile:<span style="white-space:pre-wrap"> </span>C:\temp\AND_#1.dat</div><div><span style="white-space:pre-wrap"> </span>Operation:<span style="white-space:pre-wrap"> </span>1</div>
<div><span style="white-space:pre-wrap"> </span>FiberColor:<span style="white-space:pre-wrap"> </span>(255,0,0)</div><div><span style="white-space:pre-wrap"> </span>ColorMode:<span style="white-space:pre-wrap"> </span>0</div>
<div> </div><div> BinaryFile:<span style="white-space:pre-wrap"> </span>C:\temp\NOT.dat</div><div><span style="white-space:pre-wrap"> </span>Operation:<span style="white-space:pre-wrap"> </span>3</div>
<div><span style="white-space:pre-wrap"> </span>FiberColor:<span style="white-space:pre-wrap"> </span>(255,0,0)</div><div><span style="white-space:pre-wrap"> </span>ColorMode:<span style="white-space:pre-wrap"> </span>0</div>
</div></div></div><div><div class="im"><div><br></div><div>End</div><div><br></div><div>Note:</div><div><span style="white-space:pre-wrap"> </span>Slice Orientation: 0=Coronal, 1=Axial, 2=Sagittal</div><div><span style="white-space:pre-wrap"> </span>Slice Sequencing: 0=Positive, 1=Negative</div>
<div><br></div></div><div>*** ROI Map ***</div></div><div><br></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">2013/8/7 Youngmin Huh <span dir="ltr"><<a href="mailto:ymin1123@gmail.com" target="_blank">ymin1123@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I edited map file generated by ROIEditor as below.<br>
There are two ROIs with 'or(0)' operation for the first one, and<br>
'and(1)' operation for the second one.<br>
-----------------------------------------------------<br>
*** ROI Map ***<br>
<br>
Begin<br>
ImageWidth: 240<br>
ImageHeight: 240<br>
ImageSlices: 152<br>
<br>
PixelSizeWidth: 1.000000<br>
PixelSizeHeight: 1.000000<br>
SliceThickness: 1.000000<br>
<br>
SliceOrientation: 1<br>
SliceSequencing: 0<br>
<br>
BinaryFile: E:\data\isotropic_data\ADHD\72804182\DTIstudio\test_AAL\ROImask\Amygdala_L_b.dat<br>
Operation: 0<br>
<br>
BinaryFile: E:\data\isotropic_data\ADHD\72804182\DTIstudio\test_AAL\ROImask\Amygdala_R_b.dat<br>
Operation: 1<br>
<br>
End<br>
<br>
Note:<br>
Slice Orientation: 0=Coronal, 1=Axial, 2=Sagittal<br>
Slice Sequencing: 0=Positive, 1=Negative<br>
ROI Operation: 0=OR, 1=AND, 3=NOT<br>
<br>
*** ROI Map ***<br>
-----------------------------------------------------<br>
<br>
And I load map file as Binary map format on DTI studio, but nothing happened.<br>
I can load the map file on ROIEditor, but can't load at DTI studio. I<br>
wonder why.<br>
<div><br>
Thanks,<br>
<br>
YM Huh<br>
<br>
<br>
2013/8/7 susumu mori <<a href="mailto:smoriw@gmail.com" target="_blank">smoriw@gmail.com</a>>:<br>
</div>> Hi YM,<br>
><br>
> Did you open the ROI files as BinaryMap format?<br>
> Once you save BinaryMap by RoiEditor, you have to edit the saved text file<br>
> and specify how you want to combine the multiple ROI files using AND/OR/NOT<br>
> operations.<br>
<div><div>><br>
><br>
> On Tue, Aug 6, 2013 at 10:29 PM, Youngmin Huh <<a href="mailto:ymin1123@gmail.com" target="_blank">ymin1123@gmail.com</a>> wrote:<br>
>><br>
>> Thanks for your comment!<br>
>> I'm using ROIs for fiber tracking.<br>
>><br>
>> I used ROIeditor to generate binay map files, and changed<br>
>> ROIMap_map.dat to ROIMap_map.map.<br>
>> It worked! I can load multiple RoIs at ROIEditor, but I can't figure<br>
>> out how I could load it on DTI studio.<br>
>> I tried to load map file using the "load" icon in "Fiber" tab,<br>
>> "ROI-Operation" section, but nothing happened.<br>
>> Of course I finished whole brain fiber tracking before I load ROIs.<br>
>> How could I find fibers connecting ROIs with my map file on DTI studio?<br>
>><br>
>> Thanks,<br>
>><br>
>> YM Huh<br>
>><br>
>> 2013/8/7 susumu mori <<a href="mailto:smoriw@gmail.com" target="_blank">smoriw@gmail.com</a>>:<br>
>> > Are you using ROIs for image quantification or fiber tracking?<br>
>> > From the second question, I guess you want to do a comprehensive fiber<br>
>> > tracking with a lot of ROIs.<br>
>> > If that is the case, Yajing is the right person to ask.<br>
>> > We do have command line-version of the tracking.<br>
>> ><br>
>> > Also, please take a look at RoiEditor at <a href="http://www.mristudio.org" target="_blank">www.mristudio.org</a>. It manages<br>
>> > multiple ROIs much better.<br>
>> > You can find some tips in the FAQ section.<br>
>> ><br>
>> ><br>
>> > On Tue, Aug 6, 2013 at 5:01 AM, Youngmin Huh <<a href="mailto:ymin1123@gmail.com" target="_blank">ymin1123@gmail.com</a>> wrote:<br>
>> >><br>
>> >> Hi, I'm a new user.<br>
>> >> I have been struggling with DTIstudio for few weeks.<br>
>> >> I have some questions to ask.<br>
>> >><br>
>> >> 1) how can I define multiple ROIs?<br>
>> >> I drew two ROIs with "ROI drawing" on "ROi" tab, and saved them into<br>
>> >> "binary maps".<br>
>> >> But It generated 3 dat files, but no map file (ROIMap_00.dat,<br>
>> >> ROIMap_01.dat, ROIMap_map.dat).<br>
>> >> I tried again with ROI editor, but It didn't work either. It generated<br>
>> >> only dat files.<br>
>> >> How can I generate .map file to load ROIs?<br>
>> >><br>
>> >> 2) Is there any way to automate DTI processing?<br>
>> >> I'm going to use 116 ROI masks to obtain whole brain connectivity.<br>
>> >> It seems like hard work to do all this process manually.<br>
>> >><br>
>> >> Any comment would be appreciate.<br>
>> >><br>
>> >> Thanks,<br>
>> >><br>
>> >> YM Huh<br>
>> >> _______________________________________________<br>
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