[Mristudio-users] question about segmentation of CST

[Deepa Krishnaswamy]

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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