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gregory.mccarthy
BIAC Alum
USA
26 Posts |
 Posted - Apr 22 2003 : 09:27:41 AM
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Could somebody post the steps that are currently required to convert a 'volume ROI' drawn in IRIS to a 'by slice' ROI in the format that would have been output by Overlay2? Also, how do you indicate any anatomical anchors (such as the AC) in the 'by slice' output?
-- Greg
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petty
BIAC Staff
USA
453 Posts |
Posted - Apr 22 2003 : 11:12:30 AM
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I made an html document that will guide everyone through the process of drawing ROIs in IRIS, to the ability to use them with the BIAC tools.
\\Gall\Docs\ROI\usingIRIS.html
there are also will be links to scripts that Josh wrote for using these tools, I will add them shortly
Chris
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Edited by - petty on Jun 17 2003 2:08:23 PM |
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josh.bizzell
BIAC Staff
USA
118 Posts |
Posted - Apr 23 2003 : 5:49:01 PM
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The functions Chris mentioned above are now located on \\Gall\Programs\User_Scripts\IRIStools\, with IMCONVERT having its own folder, imconv\. Anyone using older versions of these functions should now switch to these more recent, centrally located versions.
Some notes:
- IMCONVERT is used to convert most types of images BIAC uses to forms that IRIS can read (Analyze 4.0 and GIPL). XML header compatibility is currently not implemented.
- The output filename in imconvert can now contain multiple periods (e.g. N:\BIAC\Study.01\Data\Study\series002.img').
- There is a bug in the imconvert executable that sometimes causes the output image to be saved with the incorrect byte-order. Until this bug is fixed, try using the converse output type; i.e. instead of using ushort, use short.
- MSEG2ROI is used to convert ROIs drawn in IRIS into BIAC ROIs. You can trace many different ROIs (up to 255, I think) and save them all in one Analyze file with IRIS. If you label your IRIS ROIs with your preferred ROI nomenclature and save your label descriptions, you can use the label file to name your BIAC ROIs as you did with Overlay2, (e.g. MFG_R, STS_L, etc.).
- If you want to create "by slice" ROIs from volume ROIs generated by IRIS, I would recommend using Beau's ROI reslicing tool after converting the IRIS ROIs to BIAC ROIs (using MSEG2ROI) rather than creating a new label in IRIS for each slice.
- CREATESEGMASK is used to create "hard" segmentation files from probabilty maps generated by SPM or EMS using a maximum likelihood algorithm.
- Josh
*edited to reflect the recent migration to Gall from Broca |
Edited by - josh.bizzell on May 08 2003 2:32:14 PM |
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Converting ROIs from IRIS to Overlay2 format
