[Mristudio-users] question about segmentation of CST

[Dorian P.]

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
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20130130/abef6d51/attachment-0001.html