[Mristudio-users] question about segmentation of CST

[Deepa Krishnaswamy]

Hi,
As a follow up, I am also curious as to how the images in Panel A of Figure
1 in the paper mentioned below were created. Specifically, how the images
with the 3D ROIs were created.
Thanks,

Deepa

On Wed, Feb 13, 2013 at 7:09 PM, Deepa Krishnaswamy <
deepa.krishnaswamy1 at gmail.com> wrote:

> Hi,
> Yes I do understand that you would expect a lot less fibers. I am trying
> to recreate a similar looking CST as is shown in the paper 'Atlas-guided
> tract reconstruction for automated and comprehensive examination of the
> white matter anatomy.' I have been using the sample Siemens DICOM dataset,
> FA of 0.2 and an angle constraint of 40 degrees, as these were values given
> in the paper. This does not yield many fibers at all; in fact most do not
> reach the motor cortex. I've tried experimenting with the FA threshold and
> the angle constraint, but this does not seem to yield any better fibers. Is
> there anything else I can modify to yield more CST fibers? The only other
> issue I have thought of is that the flipping of the eigenvectors was
> incorrect, but I am pretty sure that there must be a Y and Z flip.
> Thanks,
>
> Deepa
>
>
> On Thu, Feb 7, 2013 at 10:48 PM, susumu mori <susumu at mri.jhu.edu> wrote:
>
>> Hi Deepa,
>>
>> if you specify the second ROI with "1", the fibers have to penetrate both
>> ROIs. So usually, you expect much less fibers.
>>
>> Susumu
>>
>>
>> On Thu, Feb 7, 2013 at 1:21 PM, Deepa Krishnaswamy <
>> deepa.krishnaswamy1 at gmail.com> wrote:
>>
>>> Hi,
>>> I'm using the Siemens DICOM sample data set. I believe that I have to
>>> choose a y and z flip, as that combination yields the correct CST fibers
>>> when I put an ROI at the cerebral peduncle.
>>> I see reasonable tracts when I use two ROIs with operation 0. There just
>>> seems to be a problem when using operation 1 for the second ROI, as there
>>> are a very small amount of fibers selected.
>>> Thanks,
>>>
>>> Deepa
>>>
>>> On Sat, Feb 2, 2013 at 4:51 PM, susumu mori <susumu at mri.jhu.edu> wrote:
>>>
>>>> One potential reason is that your vector angles are not right.
>>>> First, please make sure that your DTI data have correct fiber
>>>> orientations by using manual interactive ROI drawing and fiber tracking by
>>>> DtiStudio. For example, you can define one ROI at the cerebral peduncle and
>>>> make sure the CST trajectory reaches the motor cortex.
>>>>
>>>> If you confirm that everything is working, then it could be the problem
>>>> of your ROI file.
>>>> Do you see reasonable tracts when you use two ROIs with both operation:
>>>> 0?
>>>> If so, then you can see what happens with Operation: 1 for the second
>>>> ROI.
>>>>
>>>> On Wed, Jan 30, 2013 at 12:04 PM, Deepa Krishnaswamy <
>>>> deepa.krishnaswamy1 at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>> I have used the pipeline at
>>>>> https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_DualChannelNormalizationPipeline%3Ato transform the sample Siemens DICOM data to the JHU_MNI_SS atlas. I am
>>>>> currently trying to segment the CST using the ROI operation rules listed in
>>>>> Table 1 of 'Atlas-guided tract reconstruction for automated and
>>>>> comprehensive examination of the white matter anatomy.' I've written my own
>>>>> ROI map file that specifies the ROIs and the operations. In Table 1, there
>>>>> are two ROIs listed, two additional AND ROIs, and a list of NOT ROIs. The
>>>>> syntax I have been using for part of the map file is below:
>>>>>
>>>>> BinaryFile: pathname for ROI 1
>>>>> Operation: 0
>>>>> etc.
>>>>>
>>>>> BinaryFile: pathname for ROI 2
>>>>> Operation: 1
>>>>> etc.
>>>>>
>>>>> Binary File: pathname for first additional AND ROI
>>>>> Operation: 1
>>>>> etc.
>>>>>
>>>>> Binary File: pathname for second additional AND ROI
>>>>> Operation: 1
>>>>> etc.
>>>>>
>>>>> I do the same for all of the NOT ROIs.
>>>>>
>>>>> When I do this, there are no tracts visible. Even if I take out all
>>>>> the NOT ROIs, there are still no tracts. I am able to see tracts only if
>>>>> the operations for the first four ROIs are set to zero (OR). I know that
>>>>> this is incorrect, because the AND operation must be used for those four
>>>>> ROIs.
>>>>>
>>>>> Has anybody encountered a similar problem?
>>>>> Thanks,
>>>>>
>>>>> Deepa Krishnaswamy
>>>>>
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>>>>>
>>>>
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