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

Thu Aug 29 14:53:29 EDT 2013

Yes, you need to adjust the matrix size and voxel size.
However, what is more important is to register your image to our atlas so
that the structures defined in the atlas accurately define the
corresponding structures in your subject data.

You need to use DiffeoMap (or SPM or FSL) for the image registration.

On Thu, Aug 29, 2013 at 1:29 PM, Kotikalapudi Raviteja <
raviteja.kotikalapudi at gmail.com> wrote:

> 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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