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

Sat Aug 31 04:35:17 EDT 2013

thank you very much!

On Fri, Aug 30, 2013 at 12:23 AM, Susumu Mori <smoriw at gmail.com> wrote:

> 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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>>>>>
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