The answer is close to what Shashwath suggested, except that the "Hippocampus" segmentation is really computed at the same time as all the other subfields. For unfortunate reasons, the tail of the hippocampus that is not further subdivided in our manual training segmentations was called "Hippocampus" for lack of other good names - it really should have been "Part of the Hippocampus Tail that We Didn't Subdivide Manually".

If you want to compute the total volume of the hippocampus, you'll need to add the volume of this part, though..

Hope this helps,

Koen

On Wed, Nov 16, 2011 at 2:10 PM, Alan Francis alandarkenergy@gmail.com wrote:

Thanks Shashwath.

On Wed, Nov 16, 2011 at 2:04 PM, Shashwath shashwath123@gmail.com wrote:

...

Alan- I believe the label "hippocampus" here refers to the remaining hippo segment after the algorithm has completed  labelling of all subfields. In essence this would not be a measure that conveys very meaningful info.

Sent from my iPhone

On Nov 16, 2011, at 1:01 PM, Alan Francis alandarkenergy@gmail.com wrote:

...

Hi Koen and FreeSurfers:

I have a 3T dataset that has undergone processing using 5.1. I have also run the Hippo sub fields command. Here are my results:

[root@NeuroImage-Gamma mri]# kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt posterior_right_* posterior_Right-Hippocampus.mgz

volumeInVoxels:     right_CA1: 2473.34     right_CA2-3: 7530.08     right_CA4-DG: 4160.99     right_fimbria: 520.14     right_hippocampal_fissure: 376.772     right_presubiculum: 2780.65     right_subiculum: 4230.04     Right-Hippocampus: 2277.69

My question is :  Since these are "subfields" of the Hippocampus, should not the sum of all subregions  be equal the volume of the Right Hippocampus?

Thanks so much!

Alan Francis

Beth Israel Deaconess Medical Center, BOSTON

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At least by my reading of the Duvernoy Human Hippocampus atlas, the most anterior and posterior extents of the hippocmapus (perhaps just a slice at the tips in most scans) are almost entirely composed of the CA1 subfield. Thoughts?

Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis

On Thu, Nov 17, 2011 at 6:46 AM, Alan Francis alandarkenergy@gmail.comwrote:

Thanks Koen.

On Thu, Nov 17, 2011 at 6:14 AM, Koen Van Leemput < koen@nmr.mgh.harvard.edu> wrote:

...

The answer is close to what Shashwath suggested, except that the "Hippocampus" segmentation is really computed at the same time as all the other subfields. For unfortunate reasons, the tail of the hippocampus that is not further subdivided in our manual training segmentations was called "Hippocampus" for lack of other good names - it really should have been "Part of the Hippocampus Tail that We Didn't Subdivide Manually".

If you want to compute the total volume of the hippocampus, you'll need to add the volume of this part, though..

Hope this helps,

Koen

On Wed, Nov 16, 2011 at 2:10 PM, Alan Francis alandarkenergy@gmail.com wrote:

...

Thanks Shashwath.

On Wed, Nov 16, 2011 at 2:04 PM, Shashwath shashwath123@gmail.com

wrote:

...

...

Alan- I believe the label "hippocampus" here refers to the remaining

hippo

...

...

segment after the algorithm has completed labelling of all subfields.

In

...

...

essence this would not be a measure that conveys very meaningful info.

Sent from my iPhone

On Nov 16, 2011, at 1:01 PM, Alan Francis alandarkenergy@gmail.com wrote:

...

Hi Koen and FreeSurfers:

I have a 3T dataset that has undergone processing using 5.1. I have

also

...

...

...

run the Hippo sub fields command. Here are my results:

[root@NeuroImage-Gamma mri]# kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt

posterior_right_*

...

...

...

posterior_Right-Hippocampus.mgz

volumeInVoxels: right_CA1: 2473.34 right_CA2-3: 7530.08 right_CA4-DG: 4160.99 right_fimbria: 520.14 right_hippocampal_fissure: 376.772 right_presubiculum: 2780.65 right_subiculum: 4230.04 Right-Hippocampus: 2277.69

My question is : Since these are "subfields" of the Hippocampus,

should

...

...

...

not the sum of all subregions be equal the volume of the Right

Hippocampus?

...

...

...

Thanks so much!

Alan Francis

Beth Israel Deaconess Medical Center, BOSTON

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There is great variability between the different segmentation protocols used by different research groups, and I think people are eager for a standard to facilitate comparison and replication. By becoming part of Freesurfer, I suspect that your segmentation algorithm will become that standard.

Luckily, I think it is one of truest I've seen to conforming to the Duvernoy atlas. Whether Duvernoy's work is the appropriate standard I am not qualified to say, but he does seem to be cited quite often as the basis for the various protocols in the wild. However, there might still be some differences between Duvernoy and the scheme used by the Freesurfer subfield segmentation.

Particularly, Duvernoy seems to indicate that in the head and the tail CA1 seems to be the only subfield present in the anterior 1/3 of the head and posterior 1/3 of the tail. Looking coronally, subiculum seems to extend further laterally in the head and tail than in the body of the hippocampus. Lastly, CA1 seems to continue further medially on the superior side of the hippocampus in the head and tail than in body. CA3, by my reading of Duvernoy, seems to be tiny in the head and tail.

All these are fairly minor points. Still, I wouldn't mind some comments on these observations, as they were changes I have been proposing to make in the segmentation protocol used in my lab.

Best,

Joshua

Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805

On Thu, Nov 17, 2011 at 9:30 AM, Koen Van Leemput koen@nmr.mgh.harvard.eduwrote:

Hi Joshua,

I'm not a neuroanatomist so I can't really answer that question. My aim has just been to replicate what a human expert has given us as segmentation examples on a number of different subjects.

I know that different labs follow very different conventions for labeling the subfields manually. Perhaps someone else can chime in?

Koen

On Thu, Nov 17, 2011 at 12:18 PM, Joshua Lee jkilee@ucdavis.edu wrote:

...

At least by my reading of the Duvernoy Human Hippocampus atlas, the most anterior and posterior extents of the hippocmapus (perhaps just a slice

at

...

the tips in most scans) are almost entirely composed of the CA1 subfield. Thoughts?

Joshua

Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis

On Thu, Nov 17, 2011 at 6:46 AM, Alan Francis alandarkenergy@gmail.com wrote:

...

Thanks Koen.

On Thu, Nov 17, 2011 at 6:14 AM, Koen Van Leemput koen@nmr.mgh.harvard.edu wrote:

...

The answer is close to what Shashwath suggested, except that the "Hippocampus" segmentation is really computed at the same time as all the other subfields. For unfortunate reasons, the tail of the hippocampus that is not further subdivided in our manual training segmentations was called "Hippocampus" for lack of other good names - it really should have been "Part of the Hippocampus Tail that We Didn't Subdivide Manually".

If you want to compute the total volume of the hippocampus, you'll need to add the volume of this part, though..

Hope this helps,

Koen

On Wed, Nov 16, 2011 at 2:10 PM, Alan Francis <

alandarkenergy@gmail.com>

...

...

...

wrote:

...

Thanks Shashwath.

On Wed, Nov 16, 2011 at 2:04 PM, Shashwath shashwath123@gmail.com wrote:

...

Alan- I believe the label "hippocampus" here refers to the remaining hippo segment after the algorithm has completed labelling of all

subfields.

...

...

...

...

...

In essence this would not be a measure that conveys very meaningful

info.

...

...

...

...

...

Sent from my iPhone

On Nov 16, 2011, at 1:01 PM, Alan Francis <alandarkenergy@gmail.com

...

...

...

...

wrote:

> Hi Koen and FreeSurfers: > > I have a 3T dataset that has undergone processing using 5.1. I

have

...

...

...

...

...

> also > run the Hippo sub fields command. Here are my results: > > [root@NeuroImage-Gamma mri]#

kvlQuantifyPosteriorProbabilityImages

...

...

...

...

...

> $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt > posterior_right_* > posterior_Right-Hippocampus.mgz > > volumeInVoxels: > right_CA1: 2473.34 > right_CA2-3: 7530.08 > right_CA4-DG: 4160.99 > right_fimbria: 520.14 > right_hippocampal_fissure: 376.772 > right_presubiculum: 2780.65 > right_subiculum: 4230.04 > Right-Hippocampus: 2277.69 > > My question is : Since these are "subfields" of the Hippocampus, > should > not the sum of all subregions be equal the volume of the Right > Hippocampus? > > Thanks so much! > > Alan Francis > > Beth Israel Deaconess Medical Center, BOSTON > > _______________________________________________ > 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.

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it is addressed. If you believe this e-mail was sent to you in error and

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error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi All,

There is a large variability between labs. An extensive effort has begun for produce a "Harmonized Protocol for Hippocampal Volumetry", see:

http://www.hippocampal-protocol.net/SOPs/index.html

This group has been working on this goal for a few years. Good resources at their site, particularly showing differences between protocols.

While the project is still ongoing, its interresting.

-Timothy

On Thu, 17 Nov 2011, Joshua Lee wrote:

There is great variability between the different segmentation protocols used by different research groups, and I think people are eager for a standard to facilitate comparison and replication. By becoming part of Freesurfer, I suspect that your segmentation algorithm will become that standard.

Luckily, I think it is one of truest I've seen to conforming to the Duvernoy atlas. Whether Duvernoy's work is the appropriate standard I am not qualified to say, but he does seem to be cited quite often as the basis for the various protocols in the wild. However, there might still be some differences between Duvernoy and the scheme used by the Freesurfer subfield segmentation.

Particularly, Duvernoy seems to indicate that in the head and the tail CA1 seems to be the only subfield present in the anterior 1/3 of the head and posterior 1/3 of the tail. Looking coronally, subiculum seems to extend further laterally in the head and tail than in the body of the hippocampus. Lastly, CA1 seems to continue further medially on the superior side of the hippocampus in the head and tail than in body. CA3, by my reading of Duvernoy, seems to be tiny in the head and tail.

All these are fairly minor points. Still, I wouldn't mind some comments on these observations, as they were changes I have been proposing to make in the segmentation protocol used in my lab.

Best,

Joshua

Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805

On Thu, Nov 17, 2011 at 9:30 AM, Koen Van Leemput koen@nmr.mgh.harvard.eduwrote:

...

Hi Joshua,

I'm not a neuroanatomist so I can't really answer that question. My aim has just been to replicate what a human expert has given us as segmentation examples on a number of different subjects.

I know that different labs follow very different conventions for labeling the subfields manually. Perhaps someone else can chime in?

Koen

On Thu, Nov 17, 2011 at 12:18 PM, Joshua Lee jkilee@ucdavis.edu wrote:

...

At least by my reading of the Duvernoy Human Hippocampus atlas, the most anterior and posterior extents of the hippocmapus (perhaps just a slice

at

...

the tips in most scans) are almost entirely composed of the CA1 subfield. Thoughts?

Joshua

Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis

On Thu, Nov 17, 2011 at 6:46 AM, Alan Francis alandarkenergy@gmail.com wrote:

...

Thanks Koen.

On Thu, Nov 17, 2011 at 6:14 AM, Koen Van Leemput koen@nmr.mgh.harvard.edu wrote:

...

The answer is close to what Shashwath suggested, except that the "Hippocampus" segmentation is really computed at the same time as all the other subfields. For unfortunate reasons, the tail of the hippocampus that is not further subdivided in our manual training segmentations was called "Hippocampus" for lack of other good names - it really should have been "Part of the Hippocampus Tail that We Didn't Subdivide Manually".

If you want to compute the total volume of the hippocampus, you'll need to add the volume of this part, though..

Hope this helps,

Koen

On Wed, Nov 16, 2011 at 2:10 PM, Alan Francis <

alandarkenergy@gmail.com>

...

...

...

wrote:

...

Thanks Shashwath.

On Wed, Nov 16, 2011 at 2:04 PM, Shashwath shashwath123@gmail.com wrote: > > Alan- I believe the label "hippocampus" here refers to the remaining > hippo > segment after the algorithm has completed labelling of all

subfields.

...

...

...

...

> In > essence this would not be a measure that conveys very meaningful

info.

...

...

...

...

> > Sent from my iPhone > > On Nov 16, 2011, at 1:01 PM, Alan Francis <alandarkenergy@gmail.com

...

...

...

> wrote: > >> Hi Koen and FreeSurfers: >> >> I have a 3T dataset that has undergone processing using 5.1. I

have

...

...

...

...

>> also >> run the Hippo sub fields command. Here are my results: >> >> [root@NeuroImage-Gamma mri]#

kvlQuantifyPosteriorProbabilityImages

...

...

...

...

>> $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt >> posterior_right_* >> posterior_Right-Hippocampus.mgz >> >> volumeInVoxels: >> right_CA1: 2473.34 >> right_CA2-3: 7530.08 >> right_CA4-DG: 4160.99 >> right_fimbria: 520.14 >> right_hippocampal_fissure: 376.772 >> right_presubiculum: 2780.65 >> right_subiculum: 4230.04 >> Right-Hippocampus: 2277.69 >> >> My question is : Since these are "subfields" of the Hippocampus, >> should >> not the sum of all subregions be equal the volume of the Right >> Hippocampus? >> >> Thanks so much! >> >> Alan Francis >> >> Beth Israel Deaconess Medical Center, BOSTON >> >> _______________________________________________ >> 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.

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Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218