[Mristudio-users] FA value for regions in the corpus-callusom

[Kotikalapudi Raviteja]

Dear Susumu,

I am writing this mail in context with co-registration of DTI maps to the
T1 template. After co-registering the DTI maps (subjects and controls) to
the standard T1 template, I am able to extract the FA values for specific
ROIs. But, as you may know that all automated ROIs don't fall exactly in
the desired areas. This usually lowers my FA values as the ROI also covers
the darker areas of the map. In order to avoid that, I have done the
following:

1. Co-register the FA maps to the JHU_MNI_SS_FA_ss template.
2. Now co-register the resultant map with the T1 template.

In such a case, the accuracy of the ROIs has increased appreciably and this
has resulted in an increase in the FA values which are nearer to the
literature values.

But, is it right doing it this way? Please provide me with your thoughts on
it.

Secondly, in the MRI Cro, once we click on the ROI information button to
get the min/mean/max values for the maps, how is ROI SD values related to
it. So, am I correct in saying that if ROI SD values are nearing '0', the
process has gone perfectly well?

I would be very happy to hear from you. I thank you for your time and
consideration.

Regards,
Ravi


On Thu, Aug 29, 2013 at 9:13 PM, Susumu Mori <smoriw at gmail.com> wrote:

> There are several options depending on what you need;
>
> 1) Do fiber tracking. It seems that you obtained 5 different tracts that
> comprise the corpus callosum. As you mentioned, you can obtain one FA per
> tract. In your case, 5 FA values. Each FA value is the representative FA of
> each tract by avaraging FA values of all voxels inside a tract.
> 2) Instead of calculating a representative FA for each tract by averaging
> all voxels, you can also use the "profile" option, with which, you can
> obtain a FA value at each 2D slice (axial, sagittal, coronal separately).
> 3) As Ravi suggested, you can warp our white matter parcellation map to
> your subject image and automatically parcellate the corpus callosum into
> three regions (the genu, body, and splenium of CC).
>
> Hope one the approaches addresses your need.
>
>
>
>
> On Thu, Aug 29, 2013 at 7:32 AM, Kotikalapudi Raviteja <
> raviteja.kotikalapudi at gmail.com> wrote:
>
>> Dear Rotem,
>>
>> Though I couldn't get you completely, I understand that you need to
>> extract FA values and compare the same between subjects and controls. For
>> this purpose, you could download the JHU parcellation atlas and then use
>> MRICro to extract your ROIs using 'apply intensity to volume' option. This
>> particular ROI would then be saved and you could open it for the FA maps
>> and note down the values.
>>
>> I hope this helps, if it is related.
>>
>> Regards,
>> Ravi
>>
>>
>>
>> On Thu, Aug 29, 2013 at 4:29 PM, Rotem Saar <saar.rotem at gmail.com> wrote:
>>
>>> Dear experts,
>>>
>>> I have performed Automatic image registration to 19 subjects (who I have
>>> DTI scans for) and now about to begin fiber tracking.
>>>
>>> According to my previous anatomical results, I found volume reductions
>>> in specific areas of the corpus callosum, which were correlated to
>>> behavioral memory results. I now want to analyze the DTI data, and test for
>>> the correlations between the anatomical volume (per region, 5 in number),
>>> memory performance and FA values (per region, 5 in number).
>>>
>>> In the current working program in DTIstudio I only know how to extract a
>>> singe FA value for the corpuse if this is what I marked for the fiber
>>> tracking. I understand that I can mark a single area in the corpus each
>>> time but that will probably won't be accurate when comparing subjects...
>>>
>>> Is there any way to load a segmentation map in order for DTIstudio to
>>> compute the FA value for each region defined in the map automatically
>>> without the need to mark each time a different region ? if there is such an
>>> option, I will really appreciate if u can explain what parameters (file
>>> type ect...) it should contain.
>>>
>>> I really want to come to the tutorial, but the thing is I live in the
>>> other side of the sea:) so that won't be so easy for me to do...
>>>
>>> Thanks again for all your help
>>>  Rotem
>>>
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>>
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