open-discussion > RE: SPECT
Jan 29, 2019  10:01 AM | Larry Olson - Emory University
BioImage Suite diff-SPECT- I have quickly tested this on several old images. Initial very preliminary impression is very good, but there are some confusing issues, and there are 2 things really important to me that I can't seem to address.

This is very promising.
I like that it is quick and produces results similar to legacy ISAS. User instructions will be important.
The Hyper- hypo- coordinate results are a really useful representation.
Great to be able to control overlay parameters, including in mosaic mode.
Text/csv result saving is great feature.
I would use this by default if I could save results.

Once registration is done, it shows the Object Map as an overlay. It is not obvious that user needs to select the Tmap as an overlay from the data tree. Perhaps this should default.
Clicking on a hyper-coordinate takes the cursor to a coordinate that is not really the most intense one, and does not appear to be the center of mass of the cluster.
Mosaic "labels" does not appear to show anything useful, just the slice boundaries.
I also wonder if the underlying method is identical to ISAS or to ISAS-HN? Or perhaps a modification similar to Mayo's Statiscom method? It was previously helpful to view the Subtraction results for reference. Now I am not entirely sure of what I am looking at.

*Main issue 1:
I think the displays are always in MNI space.
It is really important to me to have results or at least the "blobs" in patient space. I can't see a way to do this. Legacy ISAS allowed applying the Inverse transformation to the perfusion blobs, which could be exported to other programs for viewing and analysis on the actual patient image in a variety of ways, but
I don't see a way to display Tmap on patient image, and
I don't see a way to export the blobs in either patient or MNI space.

*Main issue 2: I will really look forward to having access to command line tools to accomplish this. I originally modified the SPM scripts for ISAS several years ago to simplify and more or less automate the process. This worked great. Unfortunately every Matlab and SPM update broke the process. Then BIS legacy implementation came along, and it was much easier to just use that than to try to keep up with SPM and Matlab. I hope that this new BIS tool will offer some command line control again. I would like to integrate the results into my other processing results.

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Larry Olson Jan 26, 2019
Xenophon Papademetris Jan 28, 2019
Larry Olson Jan 29, 2019
Xenophon Papademetris Jan 29, 2019
Larry Olson Feb 15, 2019
Xenophon Papademetris Mar 20, 2019
Larry Olson Apr 2, 2019
Xenophon Papademetris Apr 5, 2019
Larry Olson Apr 21, 2019
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Larry Olson Apr 17, 2019
Xenophon Papademetris Feb 18, 2019