I was wondering if there is any way in anatomist to create whole brain histograms based on FA or ADC maps. Ideally I would like to exclude CSF from this histogram.
Also, is it possible to create whole slice histogram based on FA or ADC maps? Again I would like to exclude CSF from this.
Thank you for your time and help
whole brain/slice histogram from FA and ADC Maps
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Zahir Momin
- Posts: 13
- Joined: Sun Jul 18, 2004 8:35 am
In fact, there is a ROI toolbox in Anatomist. Put image in window and then click on Roi button (this button is on left of window and represent a brush). A toolbox open itself and :
- choose 'LevelSet' option
- click on 'Activate LevelSet'
- then you can see historgram of image and you can use 'Low Level' and 'High Level'.
- you can save this histogram using 'Save Histos' and a file .his will save. It is a ASCII file, you can read simply with a text editor.
If you want generate a mask, you have 2 choices :
-> first possibility :
- With this tool, you can choose value(s) to do a thresholding.
- To do a thresholding, you can use a line command 'AimsThreshold' or use an interface in BrainVISA, module 'toolbox -> Threshold'. Use this command with option -b to obtain a binary image.
-> second possibility :
- work on region in Anatomist (create session then region)
- When you use LevelSet, select 3D and clik on ROIs on window (then blue color will be pink color). Your region contains this selection.
- export this region as a mask (RoiManagment -> Region -> Export as mask)
After, you can use 'AimsMask' to obtain a new image without CSF. For instance, if you have mask.ima (mask of CSF) , map_adc.ima, map_adc_withoutCSF.ima (new image) :
AimsMask -i <map_adc.ima> -o <map_adc_withoutCSF.ima> -m <mask.ima> --inv
Isabelle
- choose 'LevelSet' option
- click on 'Activate LevelSet'
- then you can see historgram of image and you can use 'Low Level' and 'High Level'.
- you can save this histogram using 'Save Histos' and a file .his will save. It is a ASCII file, you can read simply with a text editor.
If you want generate a mask, you have 2 choices :
-> first possibility :
- With this tool, you can choose value(s) to do a thresholding.
- To do a thresholding, you can use a line command 'AimsThreshold' or use an interface in BrainVISA, module 'toolbox -> Threshold'. Use this command with option -b to obtain a binary image.
-> second possibility :
- work on region in Anatomist (create session then region)
- When you use LevelSet, select 3D and clik on ROIs on window (then blue color will be pink color). Your region contains this selection.
- export this region as a mask (RoiManagment -> Region -> Export as mask)
After, you can use 'AimsMask' to obtain a new image without CSF. For instance, if you have mask.ima (mask of CSF) , map_adc.ima, map_adc_withoutCSF.ima (new image) :
AimsMask -i <map_adc.ima> -o <map_adc_withoutCSF.ima> -m <mask.ima> --inv
Isabelle