analysis of geological CT scans

[Lukas Ro]

Hi,

i tried to figure it out on my own, but i didn't got it up to now. i hope somebody can help.

first of all, sorry if there are some mistakes in my english - it's not my motherlanguage...

i got a drilling core and i need to analize it by using a CT scanner. unfortunately i have no access to a industrial CT, however i can use a medical CT scanner. so i have a DICOM stack for doing my analysis.

my question is to analize how much volume in the core is air or gas (e.g. value= -1024 to -700 HounsfieldUnits) and how much is liquid (e.g. value -100 to +100 HU) and so on.
i tried to use Plugin -> 3D Manager. i still didn't figure it out.

i need to cut the surroundings, because around the core is air and a structure where the core is put on, i don't want to mesure.
after cutting this, i have to analize the content of the core. are there some structures filled with air or liquids or is it all stone. after that i want to have some numbers (e.g. the core has 1500cm³. in there are 12cm³ air in total)

i hope you understand what i mean, and i HOPE you can help me.

sincerely
lukas

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[John Dunsmuir]

Lukas,
   I do this sort of thing often and this is how I like to do it.  If the core cross section image in the slices is circular and aligned from slice to slice then I would suggest importing the dicoms as an image sequence, then use the circular selection tool to define the core area region of interest (ROI) that you want to measure.  Next, use the histogram tool from the analyze menu  (check the box for stack Histogram).  ImageJ will ignore the region outside the circular ROI and plot the histogram for all of the slices.  Click the List box in the plot to get the values, select all and copy. Paste the histogram into Excel or a similar program add up the pixel counts between each of the thresholds you mentioned in your note and divide each each partial sum by the total number of pixels.  This will give you the volume fraction of each of the components.  Having the histogram in Excel will allow you to easily change the thresholds to see how it changes the volume fractions.

John D.

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[Lukas Ro]

hi john,
thanks for your reply.
i've done that a few weeks before.
i was looking for an alternative, but this works pretty well for all i need.
best wishes
lukas

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[Michael Doube-4]

Hi Lukas,

Try Volume Fraction in BoneJ. Although I use BoneJ for bones, quite a few people are using it for geological samples.

http://bonej.org/volumefraction

It can handle a threshold, so have the threshold adjuster window open and the plugin will use whatever threshold values are currently selected (for you, air, water or matrix). This plugin handles ROIs, including irregular ROIs defined by a set of ROIs in the ROI manager. If you are hand-drawing a bunch of irregular ROIs on every slice (e.g. to fit the outer boundary of your core), you might find the ROI Interpolator allows you to draw every tenth or twentieth ROI and automatically fill in the rest.

http://bonej.org/utilities

Michael

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Lukas Ro [[hidden email]]
Sent: 20 April 2013 17:21
To: [hidden email]
Subject: analysis of geological CT scans

Hi,

i tried to figure it out on my own, but i didn't got it up to now. i hope somebody can help.

first of all, sorry if there are some mistakes in my english - it's not my motherlanguage...

i got a drilling core and i need to analize it by using a CT scanner. unfortunately i have no access to a industrial CT, however i can use a medical CT scanner. so i have a DICOM stack for doing my analysis.

my question is to analize how much volume in the core is air or gas (e.g. value= -1024 to -700 HounsfieldUnits) and how much is liquid (e.g. value -100 to +100 HU) and so on.
i tried to use Plugin -> 3D Manager. i still didn't figure it out.

i need to cut the surroundings, because around the core is air and a structure where the core is put on, i don't want to mesure.
after cutting this, i have to analize the content of the core. are there some structures filled with air or liquids or is it all stone. after that i want to have some numbers (e.g. the core has 1500cm³. in there are 12cm³ air in total)

i hope you understand what i mean, and i HOPE you can help me.

sincerely
lukas

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[dplatten]

Hi Lukas,

You could also write a macro to do this for you. The following will show you how many pixels are between minValue and maxValue in the current image.

// Set up the limits of the single-bin histogram
minValue = -1024;
maxValue = 500;
nBins = 1;

// Obtain the required histogram
getHistogram(values, counts, nBins, minValue, maxValue);

// Print the results to the log window
print("minValue: " + minValue);
print("maxValue: " + maxValue);
print("Number of pixels in this range:" + counts[0]);



Regards,

David

David Platten
Medical Physics Department
Northampton General Hospital
UK

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[Lukas Ro]

thanks michael,
thats a great plugin! works fine!!

lukas

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[Lukas Ro]

david,
i will try this macro thing the next days! thanks a lot for this informations!!
lukas

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