[Mristudio-users] question about segmentation of CST

[Deepa Krishnaswamy]

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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