Segmentation and volume measurements
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Segmentation and volume measurements
 
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Hello,
I am a neuroscience researcher and I am trying to analyze brain MRI images and measure the volume of different brain structures. I have been using the Segmentation Editor as part of Fiji to isolate the different structures but I do not know how to continue from there. May I ask you if anyone could please suggest me an easy technique to measure the volume of the different ROI/labels? Thank you very much for any help. Best regards, Paolo -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Diana,
In Fiji you can use the Voxel counter : On your segmented image (saved as a 8 bit color) you select with the thresholder the structure to be measured and use Plugin\Voxel counter. If your dimensions are set it gives you the number of counted pixel per image and the total volume in voxel and in the units you defined. Tha twhat we did you MRI image of mouse Hope it Help !! Eric Denarier Grenoble Institut des Neurosciences Inserm U836 Chemin Fortuné Ferrini 38700 La Tronche France Tél :33 (0)4 56 52 05 38 Fax :33 (0)4 56 52 06 57 http://neurosciences.ujf-grenoble.fr/ Le 03/04/2015 23:39, Diana, Paolo *HS a écrit : > Hello, > > I am a neuroscience researcher and I am trying to analyze brain MRI images and measure the volume of different brain structures. I have been using the Segmentation Editor as part of Fiji to isolate the different structures but I do not know how to continue from there. May I ask you if anyone could please suggest me an easy technique to measure the volume of the different ROI/labels? > > Thank you very much for any help. > > Best regards, > > Paolo > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Segmentation and volume measurements
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Hi Diana,
Measure the thresholded areas in each section. The Sum of the measured areas times the distance between measured sections returns the volume of the structure. Stoyan На 07.04.2015 10:17 "Eric Denarier" <[hidden email]> написа: > Hi Diana, > In Fiji you can use the Voxel counter : On your segmented image (saved as > a 8 bit color) you select with the thresholder the structure to be measured > and use Plugin\Voxel counter. If your dimensions are set it gives you the > number of counted pixel per image and the total volume in voxel and in the > units you defined. > Tha twhat we did you MRI image of mouse > Hope it Help !! > > Eric Denarier > Grenoble Institut des Neurosciences > Inserm U836 > Chemin Fortuné Ferrini > 38700 La Tronche > France > > > Tél :33 (0)4 56 52 05 38 > Fax :33 (0)4 56 52 06 57 > > http://neurosciences.ujf-grenoble.fr/ > > Le 03/04/2015 23:39, Diana, Paolo *HS a écrit : > >> Hello, >> >> I am a neuroscience researcher and I am trying to analyze brain MRI >> images and measure the volume of different brain structures. I have been >> using the Segmentation Editor as part of Fiji to isolate the different >> structures but I do not know how to continue from there. May I ask you if >> anyone could please suggest me an easy technique to measure the volume of >> the different ROI/labels? >> >> Thank you very much for any help. >> >> Best regards, >> >> Paolo >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Segmentation and volume measurements
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In reply to this post by ERIC
Thank you Eric for your suggestions!
I am now trying with the Segmentation Editor http://wiki.imagej.net/Segmentation_Editor to segment the original DICOM image and create an 8-bit TIFF segmented image, which I then import in the 3DRoiManager for measuring the volumes of the segmented regions http://imagejdocu.tudor.lu/doku.php?id=tutorial:working:tutorial_for_3d_roi_manager Thank you, Paolo ________________________________________ From: ImageJ Interest Group [[hidden email]] On Behalf Of Eric Denarier [[hidden email]] Sent: Tuesday, April 07, 2015 3:15 AM To: [hidden email] Subject: Re: Segmentation and volume measurements Hi Diana, In Fiji you can use the Voxel counter : On your segmented image (saved as a 8 bit color) you select with the thresholder the structure to be measured and use Plugin\Voxel counter. If your dimensions are set it gives you the number of counted pixel per image and the total volume in voxel and in the units you defined. Tha twhat we did you MRI image of mouse Hope it Help !! Eric Denarier Grenoble Institut des Neurosciences Inserm U836 Chemin Fortuné Ferrini 38700 La Tronche France Tél :33 (0)4 56 52 05 38 Fax :33 (0)4 56 52 06 57 http://neurosciences.ujf-grenoble.fr/ Le 03/04/2015 23:39, Diana, Paolo *HS a écrit : > Hello, > > I am a neuroscience researcher and I am trying to analyze brain MRI images and measure the volume of different brain structures. I have been using the Segmentation Editor as part of Fiji to isolate the different structures but I do not know how to continue from there. May I ask you if anyone could please suggest me an easy technique to measure the volume of the different ROI/labels? > > Thank you very much for any help. > > Best regards, > > Paolo > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Segmentation and volume measurements
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This plugin is useful if you create a roi on some lides of the stack.
Thereafter you can calculate the volume according to the information on the other slides of the stack. http://www.optinav.com/MeasureStack.htm El 08/04/2015 a las 05:02 p.m., Diana, Paolo *HS escribió: > Thank you Eric for your suggestions! > > I am now trying with the Segmentation Editor http://wiki.imagej.net/Segmentation_Editor to segment the original DICOM image and create an 8-bit TIFF segmented image, which I then import in the 3DRoiManager for measuring the volumes of the segmented regions http://imagejdocu.tudor.lu/doku.php?id=tutorial:working:tutorial_for_3d_roi_manager > > Thank you, > > Paolo > > ________________________________________ > From: ImageJ Interest Group [[hidden email]] On Behalf Of Eric Denarier [[hidden email]] > Sent: Tuesday, April 07, 2015 3:15 AM > To: [hidden email] > Subject: Re: Segmentation and volume measurements > > Hi Diana, > In Fiji you can use the Voxel counter : On your segmented image (saved > as a 8 bit color) you select with the thresholder the structure to be > measured and use Plugin\Voxel counter. If your dimensions are set it > gives you the number of counted pixel per image and the total volume in > voxel and in the units you defined. > Tha twhat we did you MRI image of mouse > Hope it Help !! > > Eric Denarier > Grenoble Institut des Neurosciences > Inserm U836 > Chemin Fortuné Ferrini > 38700 La Tronche > France > > > Tél :33 (0)4 56 52 05 38 > Fax :33 (0)4 56 52 06 57 > > http://neurosciences.ujf-grenoble.fr/ > > Le 03/04/2015 23:39, Diana, Paolo *HS a écrit : >> Hello, >> >> I am a neuroscience researcher and I am trying to analyze brain MRI images and measure the volume of different brain structures. I have been using the Segmentation Editor as part of Fiji to isolate the different structures but I do not know how to continue from there. May I ask you if anyone could please suggest me an easy technique to measure the volume of the different ROI/labels? >> >> Thank you very much for any help. >> >> Best regards, >> >> Paolo >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- Sincerely Mauricio Aguirre Morales -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Diana, Paolo *HS
I will use it too !!! Thanks
Eric Denarier Grenoble Institut des Neurosciences Inserm U836 Chemin Fortuné Ferrini 38700 La Tronche France Tél :33 (0)4 56 52 05 38 Fax :33 (0)4 56 52 06 57 http://neurosciences.ujf-grenoble.fr/ Le 08/04/2015 17:02, Diana, Paolo *HS a écrit : > Thank you Eric for your suggestions! > > I am now trying with the Segmentation Editor http://wiki.imagej.net/Segmentation_Editor to segment the original DICOM image and create an 8-bit TIFF segmented image, which I then import in the 3DRoiManager for measuring the volumes of the segmented regions http://imagejdocu.tudor.lu/doku.php?id=tutorial:working:tutorial_for_3d_roi_manager > > Thank you, > > Paolo > > ________________________________________ > From: ImageJ Interest Group [[hidden email]] On Behalf Of Eric Denarier [[hidden email]] > Sent: Tuesday, April 07, 2015 3:15 AM > To: [hidden email] > Subject: Re: Segmentation and volume measurements > > Hi Diana, > In Fiji you can use the Voxel counter : On your segmented image (saved > as a 8 bit color) you select with the thresholder the structure to be > measured and use Plugin\Voxel counter. If your dimensions are set it > gives you the number of counted pixel per image and the total volume in > voxel and in the units you defined. > Tha twhat we did you MRI image of mouse > Hope it Help !! > > Eric Denarier > Grenoble Institut des Neurosciences > Inserm U836 > Chemin Fortuné Ferrini > 38700 La Tronche > France > > > Tél :33 (0)4 56 52 05 38 > Fax :33 (0)4 56 52 06 57 > > http://neurosciences.ujf-grenoble.fr/ > > Le 03/04/2015 23:39, Diana, Paolo *HS a écrit : >> Hello, >> >> I am a neuroscience researcher and I am trying to analyze brain MRI images and measure the volume of different brain structures. I have been using the Segmentation Editor as part of Fiji to isolate the different structures but I do not know how to continue from there. May I ask you if anyone could please suggest me an easy technique to measure the volume of the different ROI/labels? >> >> Thank you very much for any help. >> >> Best regards, >> >> Paolo >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Segmentation and volume measurements
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Hello Eric,
If you have a label image, you can also use all the measurement tools in MorphoLibJ: https://github.com/ijpb/MorphoLibJ Cheers! ignacio On Wed, Apr 8, 2015 at 11:07 PM, Eric Denarier < [hidden email]> wrote: > I will use it too !!! Thanks > > Eric Denarier > Grenoble Institut des Neurosciences > Inserm U836 > Chemin Fortuné Ferrini > 38700 La Tronche > France > > > Tél :33 (0)4 56 52 05 38 > Fax :33 (0)4 56 52 06 57 > > http://neurosciences.ujf-grenoble.fr/ > > Le 08/04/2015 17:02, Diana, Paolo *HS a écrit : > >> Thank you Eric for your suggestions! >> >> I am now trying with the Segmentation Editor http://wiki.imagej.net/ >> Segmentation_Editor to segment the original DICOM image and create an >> 8-bit TIFF segmented image, which I then import in the 3DRoiManager for >> measuring the volumes of the segmented regions >> http://imagejdocu.tudor.lu/doku.php?id=tutorial:working: >> tutorial_for_3d_roi_manager >> >> Thank you, >> >> Paolo >> >> ________________________________________ >> From: ImageJ Interest Group [[hidden email]] On Behalf Of Eric >> Denarier [[hidden email]] >> Sent: Tuesday, April 07, 2015 3:15 AM >> To: [hidden email] >> Subject: Re: Segmentation and volume measurements >> >> Hi Diana, >> In Fiji you can use the Voxel counter : On your segmented image (saved >> as a 8 bit color) you select with the thresholder the structure to be >> measured and use Plugin\Voxel counter. If your dimensions are set it >> gives you the number of counted pixel per image and the total volume in >> voxel and in the units you defined. >> Tha twhat we did you MRI image of mouse >> Hope it Help !! >> >> Eric Denarier >> Grenoble Institut des Neurosciences >> Inserm U836 >> Chemin Fortuné Ferrini >> 38700 La Tronche >> France >> >> >> Tél :33 (0)4 56 52 05 38 >> Fax :33 (0)4 56 52 06 57 >> >> http://neurosciences.ujf-grenoble.fr/ >> >> Le 03/04/2015 23:39, Diana, Paolo *HS a écrit : >> >>> Hello, >>> >>> I am a neuroscience researcher and I am trying to analyze brain MRI >>> images and measure the volume of different brain structures. I have been >>> using the Segmentation Editor as part of Fiji to isolate the different >>> structures but I do not know how to continue from there. May I ask you if >>> anyone could please suggest me an easy technique to measure the volume of >>> the different ROI/labels? >>> >>> Thank you very much for any help. >>> >>> Best regards, >>> >>> Paolo >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Ignacio Arganda-Carreras, Ph.D. Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech Bâtiment 2 INRA Centre de Versailles-Grignon Route de St-Cyr (RD10) 78026 Versailles Cedex France Tel : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19 Website: http://sites.google.com/site/iargandacarreras/ <http://biocomp.cnb.csic.es/~iarganda/index_EN.html> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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