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>
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<div>Dear MRI Studio,</div>
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<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>
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<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>
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