[Mristudio-users] ICBM-81 complement for FMi and FMa?

[susumu mori]

Hi Cyrus,

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.

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.

On Thu, Aug 16, 2012 at 3:29 PM, Cyrus Eierud <cyrus at vtc.vt.edu> wrote:

>  Susumo,
>
> 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?
>
> Best Regards,
> Cyrus
>  ------------------------------
> *From:* mristudio-users-bounces at mristudio.org [
> mristudio-users-bounces at mristudio.org] on behalf of susumu mori [
> susumu at mri.jhu.edu]
> *Sent:* Wednesday, August 15, 2012 3:34 PM
> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support
> *Subject:* Re: [Mristudio-users] ICBM-81 complement for FMi and FMa?
>
>  Hi Cyrus,
>
>  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.
>
>  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.
>
>  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.
>
>  Susumu
>
> On Wed, Aug 15, 2012 at 2:32 PM, Cyrus Eierud <cyrus at vtc.vt.edu> wrote:
>
>>  Dear MRI Studio,
>>
>>  Thanks for your great class in July!
>> 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.
>>
>>    Best Regards,
>>  Cyrus Eierud
>> Graduate student in the LaConte Lab
>> Baylor College of Medicine, TX and
>> Virginia Tech Carilion Research Institute
>>
>>
>>
>>
>>
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