[Freesurfer] Hippocampal Subfields on 1.5 Tesla - Freesufer v. 6

[Douglas Merkitch]

Hello Freesurfer experts,

I am wondering if the new hippocampal subfields (HSF) module that will be 
included in Freesurfer v. 6 would work with 1.5 Tesla data.

Upon reviewing the mail archives, I came across a thread 
(https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35665.html) 
regarding the validity of using 1.5 Tesla T1 data with the older HSF module 
from Freesurfer v. 5.3. My takeaway from this thread is that the older module 
should work reasonably well as long as the T1 data is 1mm, regardless of 
whether the data is 1.5 or 3 Tesla (but please correct me if I am wrong!). 
Would the same apply for the new HSF module in Freesurfer v. 6 when it is 
officially released?

Any insight would be greatly appreciated!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu





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Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

[Eugenio Iglesias]

Hi Josh,
the method fits a statistical atlas of the hippocampal subfields to the image 
data. It is assumed that all subfields other than the fimbria have the same 
distribution of intensities - because they are all assumed to be gray matter. 
Therefore, most of the internal boundaries of the hippocampus rely on the prior 
given by the deformed atlas, which is mostly determined by the global 
hippocampal shape.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: Joshua Lee jki...@ucdavis.edu
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, May 1, 2014 8:03:04 PM
Subject: Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla



Thanks for the clarification Eugenio. Would saying that it relies on shape 
instead of surface be more accurate? I would like to understand better. 
Also, it is good news that there are plans to model the SLRM. 
Josh 



- 

Joshua Lee 
Doctoral Candidate 

Department of Psychology  
Center for Mind and Brain University of California, Davis 
530.747.3805 


On Mon, Apr 28, 2014 at 12:18 AM, Eugenio Iglesias  e.igles...@bcbl.eu  
wrote: 


Dear all, 
the current module in FreeSurfer works with 1mm T1 data, by relying on strong 
shape priors. So, at this point, feeding the algorithm data from a 3T scanner 
or a 1.5T scanner is pretty much the same. 
Joshua, it is indeed inaccurate to say that the method relies on a generated 
hippocampal surface, but you are definitely right regarding the SLRM: it is not 
modeled at this point (we have a new version that models it coming out 
hopefully soon!). 
Cheers, 
/Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 



- Original Message - 
From: Joshua Lee  jki...@ucdavis.edu  
To: Freesurfer support list  freesurfer@nmr.mgh.harvard.edu  
Sent: Friday, April 25, 2014 2:10:29 AM 
Subject: Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla 




Hi Alan, 

Typically subfields segmentation requires hi-resolution data (e.g. 0.4 x 0.4 mm 
in-plane resolution). The thickness of a CA subfield typically range between 
0.5-1.00 mm, but 1.5 T data does not achieve sub-millimeter resolutions. 
Further, subfield segmentation typically requires high-contrast data to discern 
the internal boundaries formed by the stratum radiatum/stratum 
lacunosum-moleculare (SLRM). I doubt that images produced on a 1.5 T magnet can 
achieve the necessary contrast. Last, and please someone correct me if what I 
say is inaccurate, but doesn't the Van Leemput method use statistical priors to 
apply label probabilities in reference to a generated hippocampal surface? This 
would imply that the method assigns label probabilities without reference to a 
subject's SLRM intensity information. For volumetry, I am somewhat skeptical 
that a method that only relies on a generated surface would be sensitive to 
group x subfield interactions; especially double dissociations in ! 


which overall volume/shape of the hippocampus may be similar across groups. 
That the that was generated from potentially low resolution, low contrast data 
cannot help the matter. Some may disagree about this though and I'd be 
interested in hearing what other people think about the matter. In general, I 
am quite optimistic about automated methods to segment the subfields. 




Joshua 







- 

Joshua K. Lee 
Doctoral Candidate 

Department of Psychology  
Center for Mind and Brain University of California, Davis 




On Thu, Apr 24, 2014 at 12:24 PM, Alan Francis  alandarkene...@gmail.com  
wrote: 



Hi Bruce and FreeSurfers: 

I have received a manuscript to review for possible publication. The authors 
have used the subfields algorithm on 1.5T scans and obtained a parcellation 
with values. They have drawn some major conclusions on the basis of the 
findings. My understanding is that this method can only be done on 3T. Is the 
1.5T results valid? 

Please advice. 

thanks, 

Alan Francis 
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Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

[Alan Francis]

Thanks Eugenio.


On Mon, Apr 28, 2014 at 3:18 AM, Eugenio Iglesias e.igles...@bcbl.euwrote:

 Dear all,
 the current module in FreeSurfer works with 1mm T1 data, by relying on
 strong shape priors. So, at this point, feeding the algorithm data from a
 3T scanner or a 1.5T scanner is pretty much the same.
 Joshua, it is indeed inaccurate to say that the method relies on a
 generated hippocampal surface, but you are definitely right regarding the
 SLRM: it is not modeled at this point (we have a new version that models it
 coming out hopefully soon!).
 Cheers,
 /Eugenio


 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu

 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


 - Original Message -
 From: Joshua Lee jki...@ucdavis.edu
 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
 Sent: Friday, April 25, 2014 2:10:29 AM
 Subject: Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla




 Hi Alan,

 Typically subfields segmentation requires hi-resolution data (e.g. 0.4 x
 0.4 mm in-plane resolution). The thickness of a CA subfield typically range
 between 0.5-1.00 mm, but 1.5 T data does not achieve sub-millimeter
 resolutions. Further, subfield segmentation typically requires
 high-contrast data to discern the internal boundaries formed by the stratum
 radiatum/stratum lacunosum-moleculare (SLRM). I doubt that images produced
 on a 1.5 T magnet can achieve the necessary contrast. Last, and please
 someone correct me if what I say is inaccurate, but doesn't the Van Leemput
 method use statistical priors to apply label probabilities in reference to
 a generated hippocampal surface? This would imply that the method assigns
 label probabilities without reference to a subject's SLRM intensity
 information. For volumetry, I am somewhat skeptical that a method that only
 relies on a generated surface would be sensitive to group x subfield
 interactions; especially double dissociations in which overall volume/shape
 of the hippocampus may be similar across groups. That the that was
 generated from potentially low resolution, low contrast data cannot help
 the matter. Some may disagree about this though and I'd be interested in
 hearing what other people think about the matter. In general, I am quite
 optimistic about automated methods to segment the subfields.




 Joshua







 -

 Joshua K. Lee
 Doctoral Candidate

 Department of Psychology 
 Center for Mind and Brain University of California, Davis




 On Thu, Apr 24, 2014 at 12:24 PM, Alan Francis  alandarkene...@gmail.com 
 wrote:



 Hi Bruce and FreeSurfers:

 I have received a manuscript to review for possible publication. The
 authors have used the subfields algorithm on 1.5T scans and obtained a
 parcellation with values. They have drawn some major conclusions on the
 basis of the findings. My understanding is that this method can only be
 done on 3T. Is the 1.5T results valid?

 Please advice.

 thanks,

 Alan Francis
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 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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Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

[Alan Francis]

Hi Joshua:

Thanks for the input. Very helpful.

Alan


On Thu, Apr 24, 2014 at 8:10 PM, Joshua Lee jki...@ucdavis.edu wrote:

 Hi Alan,

 Typically subfields segmentation requires hi-resolution data (e.g. 0.4 x
 0.4 mm in-plane resolution). The thickness of a CA subfield typically range
 between 0.5-1.00 mm, but 1.5 T data does not achieve sub-millimeter
 resolutions. Further, subfield segmentation typically requires
 high-contrast data to discern the internal boundaries formed by the stratum
 radiatum/stratum lacunosum-moleculare (SLRM). I doubt that images produced
 on a 1.5 T magnet can achieve the necessary contrast. Last, and please
 someone correct me if what I say is inaccurate, but doesn't the Van Leemput
 method use statistical priors to apply label probabilities in reference to
 a generated hippocampal surface? This would imply that the method assigns
 label probabilities without reference to a subject's SLRM intensity
 information. For volumetry, I am somewhat skeptical that a method that only
 relies on a generated surface  would be sensitive to group x subfield
 interactions; especially double dissociations in which overall volume/shape
 of the hippocampus may be similar across groups. That the that was
 generated from potentially low resolution, low contrast data cannot help
 the matter. Some may disagree about this though and I'd be interested in
 hearing what other people think about the matter. In general, I am quite
 optimistic about automated methods to segment the subfields.

 Joshua



 -
 Joshua K. Lee
 Doctoral Candidate
 Department of Psychology 
 Center for Mind and Brain
 University of California, Davis



 On Thu, Apr 24, 2014 at 12:24 PM, Alan Francis 
 alandarkene...@gmail.comwrote:

 Hi Bruce and FreeSurfers:

 I have received a manuscript to review for possible publication. The
 authors have used the subfields algorithm on 1.5T scans and obtained a
 parcellation with values. They have drawn some major conclusions on the
 basis of the findings. My understanding is that this method can only be
 done on 3T. Is the 1.5T results valid?

 Please advice.

 thanks,

 Alan Francis

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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 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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[Freesurfer] Hippocampal subfields on 1.5 Tesla

[Alan Francis]

Hi Bruce and FreeSurfers:

I have received a manuscript to review for possible publication. The
authors have used the subfields algorithm on 1.5T scans and obtained a
parcellation with values. They have drawn some major conclusions on the
basis of the findings. My understanding is that this method can only be
done on 3T. Is the 1.5T results valid?

Please advice.

thanks,

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

Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

[Joshua Lee]

Hi Alan,

Typically subfields segmentation requires hi-resolution data (e.g. 0.4 x
0.4 mm in-plane resolution). The thickness of a CA subfield typically range
between 0.5-1.00 mm, but 1.5 T data does not achieve sub-millimeter
resolutions. Further, subfield segmentation typically requires
high-contrast data to discern the internal boundaries formed by the stratum
radiatum/stratum lacunosum-moleculare (SLRM). I doubt that images produced
on a 1.5 T magnet can achieve the necessary contrast. Last, and please
someone correct me if what I say is inaccurate, but doesn't the Van Leemput
method use statistical priors to apply label probabilities in reference to
a generated hippocampal surface? This would imply that the method assigns
label probabilities without reference to a subject's SLRM intensity
information. For volumetry, I am somewhat skeptical that a method that only
relies on a generated surface  would be sensitive to group x subfield
interactions; especially double dissociations in which overall volume/shape
of the hippocampus may be similar across groups. That the that was
generated from potentially low resolution, low contrast data cannot help
the matter. Some may disagree about this though and I'd be interested in
hearing what other people think about the matter. In general, I am quite
optimistic about automated methods to segment the subfields.

Joshua



-
Joshua K. Lee
Doctoral Candidate
Department of Psychology 
Center for Mind and Brain
University of California, Davis



On Thu, Apr 24, 2014 at 12:24 PM, Alan Francis alandarkene...@gmail.comwrote:

 Hi Bruce and FreeSurfers:

 I have received a manuscript to review for possible publication. The
 authors have used the subfields algorithm on 1.5T scans and obtained a
 parcellation with values. They have drawn some major conclusions on the
 basis of the findings. My understanding is that this method can only be
 done on 3T. Is the 1.5T results valid?

 Please advice.

 thanks,

 Alan Francis

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


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