[Mristudio-users] question about segmentation of CST

[Deepa Krishnaswamy]

Hi,
Sorry I didn't write it out in the e-mail, but in the map file I do include
the NOT ROIs with the Operation set equal to 3.
Thanks,

Deepa

On Wed, Jan 30, 2013 at 1:25 PM, Dorian P. <alb.net at gmail.com> wrote:

> My understanding is that you don't have any NOT roi. Operation 1 is for
> AND ROIs. So no fibers pass in all those ROIs
>
> ROI Operation:  0=OR, 1=AND, 3=NOT, 4=Cut0, 5=Cut1, 6=AndClr, 7=NotClr,
> 8=CutClr0, 9=CutClr1
>
> Dorian
>
> 2013/1/30 Deepa Krishnaswamy <deepa.krishnaswamy1 at gmail.com>
>
>> 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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