Hi Cyrus,<div><br></div><div>I think we really can't argue which threshold is right and which is wrong. This is just a matter of pick one and use the same criteria for all subjects. One thing you should worry about is the sensitivity of your final results on the arbitrary chosen threshold.</div>
<div><br></div><div>Another approach I could recommend is, instead of applying a hard threshold and convert the probability map to 1/0 masking map (basically, you applied a cut off filter), you can apply the population-probability weighting. For example, suppose you have two pixels; one has probability 0.8 and the other has 0.5. Also, suppose the first pixel has FA = 0.6 and second one has FA = 0.4. If you use the hard cut-off, you get (0.6+0.4)/2 for FA report. If you use the probability weighting, you get [0.6 (FA) x 0.8 (probability) + 0.4 x 0.5]/[0.8+0.5]. In this way, you get FA values weighted by probability. This function is already built in RoiEditor.<br>
<br><div class="gmail_quote">On Thu, Aug 16, 2012 at 3:29 PM, Cyrus Eierud <span dir="ltr"><<a href="mailto:cyrus@vtc.vt.edu" target="_blank">cyrus@vtc.vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Susumo,
<br>
<br>
Thanks for your clear explanations about the core probability tract maps. Using the ROIEditor I selected and thresholded my ROIs (FMi and FMa) for everything between 0.001 to 1 (resulting in an acceptance of any probability above zero) to depict the ROIs. This
result also matched the FMi and FMa from your JHU-ICBM-tracts-maxprob-thr0-1mm.nii, from FSL, with the exception that the result from the ROIEditor concistently had approximately 2% more voxels by the ROIs borders. This greatly answers the question about which
tract map to use, where the ROIEditor seems to be the gold standard. May I ask a follow up question that if my (arbitrarily chosen) threshold (0.001 to 1) really is the best match to the threshold used in the ICBM-DTI-81 atlas?<br>
<br>
Best Regards,<br>
Cyrus <br>
<div style="font-size:16px;font-family:Times New Roman">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> <a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a> [<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>] on behalf of susumu mori [<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>]<br>
<b>Sent:</b> Wednesday, August 15, 2012 3:34 PM<br>
<b>To:</b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
<b>Subject:</b> Re: [Mristudio-users] ICBM-81 complement for FMi and FMa?<br>
</font><br>
</div>
<div></div>
<div>Hi Cyrus,
<div><br>
</div>
<div>When we parcellate the white matter, there are two different approaches. This is somewhat similar to geological maps, which also contain two types of information. One is location boarders and the other is road maps. For example, City of Baltimore or Maryland
State are defined by boarders. On the other hand Route 40 penetrates multiple cities and states. </div>
<div><br>
</div>
<div>Our parcellation maps (WMPM) are similar to the location boarders. Based on image contrasts, we tried to define structures. If we look at the posterior limb of the internal capsule, we can define it based on FA contrasts (differentiate it from thalamus
and putamen), color (fiber orientation, differentiate it from the anterior limb and retrolenticular internal capsule), and anatomical landmarks. We also have white matter definitions based on tractography, which is similar to the road map in the above analogy.
The corticospinal tract penetrates the pons, a portion of the posterior limb of the internal capsule, and the corona radiata.</div>
<div><br>
</div>
<div>For FMi and FMa, they are divided into several portions in our WMPM. However, I believe that FMi and FMa are a part of the fibers provided in "Tracts" option in the "Atlas" section of the right column of RoiEditor. Please select "JHU_MNI_GA" as the atlas
in the "Atlas" section and click "open" in the "Tract" section. You can load and look at the population-probabilistic locations. They are generated from JHU DTI data, but the coordinates are quite compatible with ICBM-MNI. In the RoiEditor directory, you can
also find the 3D raw files of these fibers.</div>
<div><br>
</div>
<div>Susumu</div>
<div><br>
<div class="gmail_quote">On Wed, Aug 15, 2012 at 2:32 PM, Cyrus Eierud <span dir="ltr">
<<a href="mailto:cyrus@vtc.vt.edu" target="_blank">cyrus@vtc.vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;color:rgb(0,91,0);font-size:16px;font-family:Calibri,sans-serif">
<div>Dear MRI Studio,</div>
<div><br>
</div>
<div>Thanks for your great class in July!</div>
<div>Working with a meta analysis of WM regions I decided to use the ICBM-81 as the gold standard, which all other articles has to match even if coordinates are used. However, ICBM-81 does not include the important forceps minor (FMi) nor forceps major (FMa)
regions. I found that in FSL there are JHU-ICBM-tracts-maxprob-thr0-1mm.nii, JHU-ICBM-tracts-maxprob-thr25-1mm.nii and JHU-ICBM-tracts-maxprob-thr50-1mm.nii that do include both FMi and FMa, but with different thresholds. I thought I could create my own map
by merging one of the other 3 maps with the ICBM-81, but I would like FMi and FMa to have a comparable threshold to the original threshold of ICBM-81. In my study I need the parcellated spatial ROI distributions to have the same threshold (including for FMi
and FMa). Can you recommend which FMi/FMa map I should use to merge with the ICBM-81 to get a complete white matter parcellation map? In addition, I don't necessarily need to merge the additional map to the ICBM-81. It is also okay if you tell me which map,
which includes FMi and FMa, that has the most comparable threshold as the ICBM-81 map.</div>
<div><br>
</div>
<div>
<div>
<div>
<div>
<div style="font-family:'Times New Roman'">Best Regards,</div>
<div style="font-family:'Times New Roman'">
<div>Cyrus Eierud </div>
<div>Graduate student in the LaConte Lab</div>
<div>Baylor College of Medicine, TX and</div>
<div>Virginia Tech Carilion Research Institute</div>
</div>
</div>
</div>
</div>
</div>
<div><br>
</div>
<div> </div>
<div><br>
</div>
<div><br>
</div>
</div>
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