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

Thu Aug 29 13:29:09 EDT 2013

Hi Susumu,

In that case, while I am having an FA map of 128x128x70 with slice
thickness of 1mm, I could resample it to 181x217x181 with slice thinkness
1mm and extract the ROIs? i thank you for your reply.

Regards,
Ravi

On Thu, Aug 29, 2013 at 10:47 PM, Susumu Mori <smoriw at gmail.com> wrote:

> Hi Ravi,
>
> if you are interested in measurements of FA values are specific white
> matter areas, why do you need to register DTI to  T1?
> You can directly apply the atlas to DTI.
>
>
> On Thu, Aug 29, 2013 at 12:39 PM, Kotikalapudi Raviteja <
> raviteja.kotikalapudi at gmail.com> wrote:
>
>> 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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