Dear List,
I recently posted the message you see below.
I currently compare the segmentation results of different segementation algorithms and FreeSurfer always yields the least accurate results. Because I still have difficulties to decide which of the labels in the aseg.mgz files should be considered gray matter, I have the feeling, the bad results I am getting for FreeSufer might be caused by not including all relevant gray matter segments.
So, I would very much appreaciate any help on deciding which of the labels in the aseg.mgz file belong to gray matter!
With kind regards Lucas Eggert
-------- Original-Nachricht -------- Betreff: [Freesurfer] How to determine gray matter in the aseg.mgz Datum: Tue, 03 May 2011 17:26:55 +0200 Von: Lucas Eggert leggert@Uni-Osnabrueck.DE An: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Dear Experts,
I would like to generate a gray matter mask using the aparc+aseg.mgz file.
Now, my question is whether there exists a file in addition to the FreeSurferColorLUT.txt file, which more explicitly, i. e., withouth the abbreviations, explains the labels, because I find it hard to decide whether, e. g., "Left-VentralDC", "Line1", "LeftmOg", or "Left-Interior" belong to gray matter, or not (to name only a few of those labels I cannot clearly classify).
Or is there a easier way to create a gray matter mask?
Thank you very much in advance!
Best regards, Lucas Eggert
Hi Lucas,
To know if a given structure is gray or white matter you can look in any reasonable anatomy textbook. In any case, the question itself is somewhat ill-posed, because some of the subcortical structures have heterogeneous tissue composition and can't really be labeled entirely as gray matter, even macroscopically. The most notable examples are perhaps the thalamus and hippocampus, but the same applies to other structures too.
Anyway, if you really want to make a hard distinction, you can call then caudate, putamen, pallidum, amygdala, accumbens, hippocampus and thalamus as gray matter. The region defined as ventral diencephalon is very heterogeneous and I would not classify it either as GM or WM, as it includes mamillary bodies, tuber cinereum/infundibulum (but not hypophysis), some hypothalamic nuclei near the lateral and inferior walls of the 3rd ventricle and sometimes fragments of the optic tracts (but not chiasm, which has its own label). It also includes parts of the mesencephalon (e.g. part of the cerebral crux, part of the substantia nigra and rubra).
Importantly, if you are comparing algorithms, you have to be sure they are reporting the same thing. For instance, it's fairly common to run SPM or FSL/FAST segmentation, then sum the GM voxels within a region defined from an atlas. If you do this for, say, caudate or thalamus, you'll get the volume of what the algorithm classified as GM within the structure you selected. FreeSurfer (and, e.g. FSL/FIRST), on the other hand, will segment and report the volume of the structure as a whole, including all what it contains. A direct comparison, thus, is not valid.
Hope this helps!
All the best,
Anderson
On 28/08/11 02:53, Lucas Eggert wrote:
Dear List,
I recently posted the message you see below.
I currently compare the segmentation results of different segementation algorithms and FreeSurfer always yields the least accurate results. Because I still have difficulties to decide which of the labels in the aseg.mgz files should be considered gray matter, I have the feeling, the bad results I am getting for FreeSufer might be caused by not including all relevant gray matter segments.
So, I would very much appreaciate any help on deciding which of the labels in the aseg.mgz file belong to gray matter!
With kind regards Lucas Eggert
-------- Original-Nachricht -------- Betreff: [Freesurfer] How to determine gray matter in the aseg.mgz Datum: Tue, 03 May 2011 17:26:55 +0200 Von: Lucas Eggert leggert@Uni-Osnabrueck.DE An: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Dear Experts,
I would like to generate a gray matter mask using the aparc+aseg.mgz file.
Now, my question is whether there exists a file in addition to the FreeSurferColorLUT.txt file, which more explicitly, i. e., withouth the abbreviations, explains the labels, because I find it hard to decide whether, e. g., "Left-VentralDC", "Line1", "LeftmOg", or "Left-Interior" belong to gray matter, or not (to name only a few of those labels I cannot clearly classify).
Or is there a easier way to create a gray matter mask?
Thank you very much in advance!
Best regards, Lucas Eggert
-- Lucas Eggert, M.Sc. Institute of Cognitive Science University of Osnabrueck Albrechtstrasse 28 D-49076 Osnabrueck Germany
Phone: +49-541-969-44-28 Website:http://www.cogsci.uni-osnabrueck.de/~leggert/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Dear Anderson Winkler,
thank you very much for your quick response and your very helpful comments!
To know if a given structure is gray or white matter you can look in any reasonable anatomy textbook.
That is ture, of course; however, my problem is rather to match labels like "LeftmOg" in the aseg.mgz file to anatomical structures.
In any case, the question itself is somewhat ill-posed, because some of the subcortical structures have heterogeneous tissue composition and can't really be labeled entirely as gray matter, even macroscopically. The most notable examples are perhaps the thalamus and hippocampus, but the same applies to other structures too.
That is totally true. Nevertheless, for a comparison between different segmentation methods, if you would like to compare e. g. total gray matter volume, it is important to know, which of the labels should rather be regarded as gray matter and which should be regarded as something else. But as you mention below, a direct comparison between different segmentation methods might not be valid --- Thanks for this important hint!
But then, I am a bit suprised, anyway: I am not familiar with the method used by FreeSurfer for (sub)cortical segmentation; but could you, in simple words describe shortly, how FreeSurfer does the segmentation, if not voxel-vise, that is, how does FreeSurfer define a whole structure (see your comment below)? That would be of great help for the upcoming discussion of the results for the evaluation of different segmentation methods.
Anyway, if you really want to make a hard distinction, you can call then caudate, putamen, pallidum, amygdala, accumbens, hippocampus and thalamus as gray matter. The region defined as ventral diencephalon is very heterogeneous and I would not classify it either as GM or WM, as it includes mamillary bodies, tuber cinereum/infundibulum (but not hypophysis), some hypothalamic nuclei near the lateral and inferior walls of the 3rd ventricle and sometimes fragments of the optic tracts (but not chiasm, which has its own label). It also includes parts of the mesencephalon (e.g. part of the cerebral crux, part of the substantia nigra and rubra).
Importantly, if you are comparing algorithms, you have to be sure they are reporting the same thing. For instance, it's fairly common to run SPM or FSL/FAST segmentation, then sum the GM voxels within a region defined from an atlas. If you do this for, say, caudate or thalamus, you'll get the volume of what the algorithm classified as GM within the structure you selected. FreeSurfer (and, e.g. FSL/FIRST), on the other hand, will segment and report the volume of the structure as a whole, including all what it contains. A direct comparison, thus, is not valid.
With kind regards Lucas Eggert
Hi Lucas,
It seems you are looking at the FreeSurferColorLUT.txt. Not all these labels are in the aseg.mgz file. Try looking at the aseg.stats file, in the subdirectory stats of each directory of your subjects. The labels there are the ones in the aseg.mgz, and have friendly names.
For the segmentation, FS still works voxelwise, but it's objective is to identify each structure as a whole, whereas SPM and FSL/FAST attempt to classify each voxel as being GM, WM or CSF. A short description of the method in FS is here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#... You may want also to have a look at this paper: http://dx.doi.org/10.1016/S0896-6273(02)00569-X
Hope this helps!
All the best,
Anderson
On 29/08/11 03:38, Lucas Eggert wrote:
Dear Anderson Winkler,
thank you very much for your quick response and your very helpful comments!
To know if a given structure is gray or white matter you can look in any reasonable anatomy textbook.
That is ture, of course; however, my problem is rather to match labels like "LeftmOg" in the aseg.mgz file to anatomical structures.
In any case, the question itself is somewhat ill-posed, because some of the subcortical structures have heterogeneous tissue composition and can't really be labeled entirely as gray matter, even macroscopically. The most notable examples are perhaps the thalamus and hippocampus, but the same applies to other structures too.
That is totally true. Nevertheless, for a comparison between different segmentation methods, if you would like to compare e. g. total gray matter volume, it is important to know, which of the labels should rather be regarded as gray matter and which should be regarded as something else. But as you mention below, a direct comparison between different segmentation methods might not be valid --- Thanks for this important hint!
But then, I am a bit suprised, anyway: I am not familiar with the method used by FreeSurfer for (sub)cortical segmentation; but could you, in simple words describe shortly, how FreeSurfer does the segmentation, if not voxel-vise, that is, how does FreeSurfer define a whole structure (see your comment below)? That would be of great help for the upcoming discussion of the results for the evaluation of different segmentation methods.
Anyway, if you really want to make a hard distinction, you can call then caudate, putamen, pallidum, amygdala, accumbens, hippocampus and thalamus as gray matter. The region defined as ventral diencephalon is very heterogeneous and I would not classify it either as GM or WM, as it includes mamillary bodies, tuber cinereum/infundibulum (but not hypophysis), some hypothalamic nuclei near the lateral and inferior walls of the 3rd ventricle and sometimes fragments of the optic tracts (but not chiasm, which has its own label). It also includes parts of the mesencephalon (e.g. part of the cerebral crux, part of the substantia nigra and rubra).
Importantly, if you are comparing algorithms, you have to be sure they are reporting the same thing. For instance, it's fairly common to run SPM or FSL/FAST segmentation, then sum the GM voxels within a region defined from an atlas. If you do this for, say, caudate or thalamus, you'll get the volume of what the algorithm classified as GM within the structure you selected. FreeSurfer (and, e.g. FSL/FIRST), on the other hand, will segment and report the volume of the structure as a whole, including all what it contains. A direct comparison, thus, is not valid.
With kind regards Lucas Eggert
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Lucas
the problem can be one of definitions. For example the FreeSurfer definition of the thalamus extends into the lateral thalamic nuclei that look a lot like wm, whereas others don't necessarily. Thus it's hard to compare apples to apples.
cheers Bruce On Mon, 29 Aug 2011, Anderson Winkler wrote:
Hi Lucas,
It seems you are looking at the FreeSurferColorLUT.txt. Not all these labels are in the aseg.mgz file. Try looking at the aseg.stats file, in the subdirectory stats of each directory of your subjects. The labels there are the ones in the aseg.mgz, and have friendly names.
For the segmentation, FS still works voxelwise, but it's objective is to identify each structure as a whole, whereas SPM and FSL/FAST attempt to classify each voxel as being GM, WM or CSF. A short description of the method in FS is here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#... You may want also to have a look at this paper: http://dx.doi.org/10.1016/S0896-6273(02)00569-X
Hope this helps!
All the best,
Anderson
On 29/08/11 03:38, Lucas Eggert wrote: Dear Anderson Winkler,
thank you very much for your quick response and your very helpful comments! To know if a given structure is gray or white matter you can look in any reasonable anatomy textbook. That is ture, of course; however, my problem is rather to match labels like "LeftmOg" in the aseg.mgz file to anatomical structures. In any case, the question itself is somewhat ill-posed, because some of the subcortical structures have heterogeneous tissue composition and can't really be labeled entirely as gray matter, even macroscopically. The most notable examples are perhaps the thalamus and hippocampus, but the same applies to other structures too. That is totally true. Nevertheless, for a comparison between different segmentation methods, if you would like to compare e. g. total gray matter volume, it is important to know, which of the labels should rather be regarded as gray matter and which should be regarded as something else. But as you mention below, a direct comparison between different segmentation methods might not be valid --- Thanks for this important hint! But then, I am a bit suprised, anyway: I am not familiar with the method used by FreeSurfer for (sub)cortical segmentation; but could you, in simple words describe shortly, how FreeSurfer does the segmentation, if not voxel-vise, that is, how does FreeSurfer define a whole structure (see your comment below)? That would be of great help for the upcoming discussion of the results for the evaluation of different segmentation methods. Anyway, if you really want to make a hard distinction, you can call then caudate, putamen, pallidum, amygdala, accumbens, hippocampus and thalamus as gray matter. The region defined as ventral diencephalon is very heterogeneous and I would not classify it either as GM or WM, as it includes mamillary bodies, tuber cinereum/infundibulum (but not hypophysis), some hypothalamic nuclei near the lateral and inferior walls of the 3rd ventricle and sometimes fragments of the optic tracts (but not chiasm, which has its own label). It also includes parts of the mesencephalon (e.g. part of the cerebral crux, part of the substantia nigra and rubra). Importantly, if you are comparing algorithms, you have to be sure they are reporting the same thing. For instance, it's fairly common to run SPM or FSL/FAST segmentation, then sum the GM voxels within a region defined from an atlas. If you do this for, say, caudate or thalamus, you'll get the volume of what the algorithm classified as GM within the structure you selected. FreeSurfer (and, e.g. FSL/FIRST), on the other hand, will segment and report the volume of the structure as a whole, including all what it contains. A direct comparison, thus, is not valid. With kind regards Lucas Eggert
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Dear Bruce Fischl,
thank you very much for your comment!
So, as Anderson Winkler already mentioned, a comparison of the segmentation results of e. g. SPM and FreeSufer might not be valid, as FreeSufer might not be designed to conduct e. g. VBM-analysis in the first place. Nevertheless, I think to systematically evaluate different segmentation algorithms, as e. g. SPM, FSL, and FreeSufer, and compare their results, might still be of use to the community, because different algortihms might have different 'optimal domains' for their application (see e. g. Klauschen et al. 2009, HBM). Or would you rather discourage me to compare FreeSufers segmentation to any of the other commonly used software tools at all?
All the best Lucas Eggert
Hi Lucas
the problem can be one of definitions. For example the FreeSurfer definition of the thalamus extends into the lateral thalamic nuclei that look a lot like wm, whereas others don't necessarily. Thus it's hard to compare apples to apples.
cheers Bruce On Mon, 29 Aug 2011, Anderson Winkler wrote:
Hi Lucas,
It seems you are looking at the FreeSurferColorLUT.txt. Not all these labels are in the aseg.mgz file. Try looking at the aseg.stats file, in the subdirectory stats of each directory of your subjects. The labels there are the ones in the aseg.mgz, and have friendly names.
For the segmentation, FS still works voxelwise, but it's objective is to identify each structure as a whole, whereas SPM and FSL/FAST attempt to classify each voxel as being GM, WM or CSF. A short description of the method in FS is here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#...
You may want also to have a look at this paper: http://dx.doi.org/10.1016/S0896-6273(02)00569-X
Hope this helps!
All the best,
Anderson
On 29/08/11 03:38, Lucas Eggert wrote: Dear Anderson Winkler,
thank you very much for your quick response and your veryhelpful comments!
To know if a given structure is gray or white matter youcan look in any reasonable anatomy textbook.
That is ture, of course; however, my problem is rather to matchlabels like "LeftmOg" in the aseg.mgz file to anatomical structures. In any case, the question itself is somewhat ill-posed, because some of the subcortical structures have heterogeneous tissue composition and can't really be labeled entirely as gray matter, even macroscopically. The most notable examples are perhaps the thalamus and hippocampus, but the same applies to other structures too.
That is totally true. Nevertheless, for a comparison betweendifferent segmentation methods, if you would like to compare e. g. total gray matter volume, it is important to know, which of the labels should rather be regarded as gray matter and which should be regarded as something else. But as you mention below, a direct comparison between different segmentation methods might not be valid --- Thanks for this important hint!
But then, I am a bit suprised, anyway: I am not familiar withthe method used by FreeSurfer for (sub)cortical segmentation; but could you, in simple words describe shortly, how FreeSurfer does the segmentation, if not voxel-vise, that is, how does FreeSurfer define a whole structure (see your comment below)? That would be of great help for the upcoming discussion of the results for the evaluation of different segmentation methods.
Anyway, if you really want to make a hard distinction,you can call then caudate, putamen, pallidum, amygdala, accumbens, hippocampus and thalamus as gray matter. The region defined as ventral diencephalon is very heterogeneous and I would not classify it either as GM or WM, as it includes mamillary bodies, tuber cinereum/infundibulum (but not hypophysis), some hypothalamic nuclei near the lateral and inferior walls of the 3rd ventricle and sometimes fragments of the optic tracts (but not chiasm, which has its own label). It also includes parts of the mesencephalon (e.g. part of the cerebral crux, part of the substantia nigra and rubra).
Importantly, if you are comparing algorithms, you have tobe sure they are reporting the same thing. For instance, it's fairly common to run SPM or FSL/FAST segmentation, then sum the GM voxels within a region defined from an atlas. If you do this for, say, caudate or thalamus, you'll get the volume of what the algorithm classified as GM within the structure you selected. FreeSurfer (and, e.g. FSL/FIRST), on the other hand, will segment and report the volume of the structure as a whole, including all what it contains. A direct comparison, thus, is not valid.
With kind regards Lucas Eggert
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Anderson Winkler -
Bruce Fischl -
Lucas Eggert