[Mristudio-users] Question about map file operations

[Deepa Krishnaswamy]

Hi,
This is a follow up question from an e-mail I sent about two weeks ago
about track segmentation.
I have been comparing results of fiber tracks using two different methods.
The first method uses the map files to specify the ROI operations in
DTIStudio. These tracks were then saved and converted to .trk format. The
second method converts the ROIs from dat to nii, and the whole brain track
is converted to .trk format. The fiber tracks are then extracted using
custom made functions. I have noticed slight differences between the
results of the tracks, the most apparent being the CST when all of the ROIs
are used. For instance, I could see with MATLAB, 1245 fibers were
extracted, and with DTI Studio the number is 1009. Has a similar issue been
encountered by anyone?
Thanks,

Deepa


On Thu, May 2, 2013 at 3:11 PM, Deepa Krishnaswamy <
deepa.krishnaswamy1 at gmail.com> wrote:

> Hi,
> This is a follow up question from an e-mail I sent about two weeks ago
> about track segmentation.
> I have been comparing results of fiber tracks using two different methods.
> The first method uses the map files to specify the ROI operations in
> DTIStudio. These tracks were then saved and converted to .trk format. The
> second method converts the ROIs from dat to nii, and the whole brain track
> is converted to .trk format. The fiber tracks are then extracted using
> custom made functions. I have noticed slight differences between the
> results of the tracks, the most apparent being the CST when all of the ROIs
> are used. I have attached a powerpoint which show the differences in the
> number of fibers obtained from DTI Studio vs MATLAB. You can see that with
> MATLAB, 1245 fibers were extracted, and with DTI Studio the number is 1009.
> Has this issue been encountered by anyone?
> Thanks,
>
> Deepa
>
>
> On Thu, Apr 18, 2013 at 10:58 AM, Deepa Krishnaswamy <
> deepa.krishnaswamy1 at gmail.com> wrote:
>
>> Hi,
>> So I combined the ROIs as mentioned above (did this in MATLAB as I found
>> it easier); these were for the left frontal and left temporal lobes (used
>> to extract the SLF-t). Only a few fibers were extracted, and I am unsure as
>> to why there are so few. I'm using the processed data (Subject_LDDMM.d) for
>> tractography.
>> Also I noticed in the paper (also mentioned above), there are ROIs listed
>> for major tracts, such as CST, SLF, etc. How can this one ROI be used to
>> extract a tract? I noticed the results using the one ROI for the CST, and
>> the actual list of ROIs are very different.
>> Thanks,
>>
>> Deepa
>>
>>
>> On Mon, Apr 15, 2013 at 7:40 PM, susumu mori <susumu at mri.jhu.edu> wrote:
>>
>>> Good question.
>>> There may be a clever way to do it, but I would combine the ROI #1-3 and
>>> ROI#4-6 first and create two ROI masking files.
>>>
>>>
>>> On Mon, Apr 15, 2013 at 4:46 PM, Deepa Krishnaswamy <
>>> deepa.krishnaswamy1 at gmail.com> wrote:
>>>
>>>> Hi,
>>>> Thanks Durai, you are absolutely correct. It seems that using two ROIs
>>>> (first as AND, second as OR) is exactly the same as using the second ROI as
>>>> an OR.
>>>> Another question, if I am trying to implement something like (ROI1 OR
>>>> ROI2 OR ROI3) AND (ROI4 OR ROI5 OR ROI6), how would this actually be done
>>>> using the map file? Of course I could do this by manually combining ROI1, 2
>>>> and 3 together, as well as 4,5 and 6, but I don't want to do that.
>>>> Thanks,
>>>>
>>>> Deepa
>>>>
>>>>
>>>> On Mon, Apr 15, 2013 at 2:55 PM, Durai Arasan <durai23 at gmail.com>wrote:
>>>>
>>>>>
>>>>>> If say I happen to put the first operation as AND, and the second
>>>>>> operation as OR, I still obtain a fiber bundle. I don't understand what
>>>>>> this actually means logically.
>>>>>>
>>>>>
>>>>> If the fiber bundle obtained is the same as that obtained if you just
>>>>> draw one OR roi, then it means the result of the first AND operation was a
>>>>> null roi. I think the logical ROI operations in DTI studio take a "null
>>>>> roi" as the default argument when a roi is not provided explicitly.
>>>>>
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>>>>
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