Re: [Freesurfer] Difference in hippocampal volume between scanners

[Jessica Liu]

Alright, thanks for all of your input!

Jessica

2011/6/24 Bruce Fischl 

> Hi Jessica
>
> yes, probably. With so many differences (sequence, field strength, coil) it
> will be really hard to get anything out of a combined dataset.
>
> sorry
> Bruce
>
> On Fri, 24 Jun 2011, Jessica Liu wrote:
>
>  Hi Dr. Fischl,
>>
>> Thanks for your comments.  The aim of my study is to analyze the brain
>> volume in AD subjects.  Most of the study was scanned on the 1.5T
>> (single-channel head coil) with a few subjects rescanned on the 3T
>> (12-channel head coil), so we would like to compare the brain volume of
>> the
>> same subject on both scanners.  In addition, the protocols on the two
>> scanners didn't match exactly due to the limitations of our over
>> 15-years-old 1.5T scanner (i.e. non-isotropic voxel size).  From your
>> comment, I gather that the 1.5T data is rather imprecise/unreliable.
>> Since
>> I'm a summer student, do you recommend that I should concentrate on
>> analyzing the 3T data only, and hopefully all of the subjects can be
>> rescanned on the 3T?  Thanks!
>>
>> Jessica Liu
>>
>> 2011/6/23 Bruce Fischl 
>>  Hi Jessica,
>>
>>  the 1.5t scan looks kind of washed out and low contrast, but of
>>  course it's hard to tell from an image. The 3T looks much
>>  crisper. Were the sequence parameters matched? I'm not sure what
>>  you're trying to show with this. The 3T multi-channel scan will
>>  have a much, much higher SNR than the 1.5T single channel, so
>>  the results will not at all be comparable.
>>
>>  Bruce
>>
>>
>>  On Thu, 23 Jun 2011, Jessica Liu wrote:
>>
>>  Looking at the scans (attached, 3T on the left and 1.5T on
>>  the right, yellow
>>  hippocampus), I think you've made a good point.  More
>>  comments are much
>>  appreciated, thanks!
>>
>>  Jessica Liu
>>
>>  2011/6/23 Pedro Paulo de Magalhães Oliveira Junior
>>  
>>   This is not normal. Maybe you should check the aseg
>>  volume for
>>   improper segmentation.
>>
>>
>>  On Thu, Jun 23, 2011 at 19:27, Jessica Liu
>>  
>>  wrote:
>>  Hi everyone!
>>
>>  I'm currently a summer student working at a lab which uses
>>  Freesurfer to measure hippocampal volumes.  I noticed that
>>  scanning the same patient first on a GE 3T (Multi-channel
>>  head
>>  coil) and then a GE 1.5T (single-channel head coil) 24
>>  hours
>>  later resulted in a 30% increase in the left hippocampus
>>  volume
>>  and a 18% increase for the right hippocampus based on the
>>  values
>>  in aseg.stats.  Can anyone please comment on this and
>>  explain
>>  the large discrepancies?  Thanks!
>>
>>  Jessica Liu
>>
>>  __**_
>>  Freesurfer mailing list
>>  Freesurfer@nmr.mgh.harvard.edu
>>  
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>
>>
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>>  
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Re: [Freesurfer] Difference in hippocampal volume between scanners

[Bruce Fischl]

Hi Jessica

yes, probably. With so many differences (sequence, field strength, coil) 
it will be really hard to get anything out of a combined dataset.


sorry
Bruce
On Fri, 24 
Jun 2011, Jessica Liu wrote:



Hi Dr. Fischl,

Thanks for your comments.  The aim of my study is to analyze the brain
volume in AD subjects.  Most of the study was scanned on the 1.5T
(single-channel head coil) with a few subjects rescanned on the 3T
(12-channel head coil), so we would like to compare the brain volume of the
same subject on both scanners.  In addition, the protocols on the two
scanners didn't match exactly due to the limitations of our over
15-years-old 1.5T scanner (i.e. non-isotropic voxel size).  From your
comment, I gather that the 1.5T data is rather imprecise/unreliable.  Since
I'm a summer student, do you recommend that I should concentrate on
analyzing the 3T data only, and hopefully all of the subjects can be
rescanned on the 3T?  Thanks!

Jessica Liu

2011/6/23 Bruce Fischl 
  Hi Jessica,

  the 1.5t scan looks kind of washed out and low contrast, but of
  course it's hard to tell from an image. The 3T looks much
  crisper. Were the sequence parameters matched? I'm not sure what
  you're trying to show with this. The 3T multi-channel scan will
  have a much, much higher SNR than the 1.5T single channel, so
  the results will not at all be comparable.

  Bruce


  On Thu, 23 Jun 2011, Jessica Liu wrote:

  Looking at the scans (attached, 3T on the left and 1.5T on
  the right, yellow
  hippocampus), I think you've made a good point.  More
  comments are much
  appreciated, thanks!

  Jessica Liu

  2011/6/23 Pedro Paulo de Magalhães Oliveira Junior
  
       This is not normal. Maybe you should check the aseg
  volume for
       improper segmentation.


  On Thu, Jun 23, 2011 at 19:27, Jessica Liu
  
  wrote:
  Hi everyone!

  I'm currently a summer student working at a lab which uses
  Freesurfer to measure hippocampal volumes.  I noticed that
  scanning the same patient first on a GE 3T (Multi-channel
  head
  coil) and then a GE 1.5T (single-channel head coil) 24
  hours
  later resulted in a 30% increase in the left hippocampus
  volume
  and a 18% increase for the right hippocampus based on the
  values
  in aseg.stats.  Can anyone please comment on this and
  explain
  the large discrepancies?  Thanks!

  Jessica Liu

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  Compliance HelpLine at
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Re: [Freesurfer] Difference in hippocampal volume between scanners

[Jessica Liu]

Hi Dr. Fischl,

Thanks for your comments.  The aim of my study is to analyze the brain
volume in AD subjects.  Most of the study was scanned on the 1.5T
(single-channel head coil) with a few subjects rescanned on the 3T
(12-channel head coil), so we would like to compare the brain volume of the
same subject on both scanners.  In addition, the protocols on the two
scanners didn't match exactly due to the limitations of our over
15-years-old 1.5T scanner (i.e. non-isotropic voxel size).  From your
comment, I gather that the 1.5T data is rather imprecise/unreliable.  Since
I'm a summer student, do you recommend that I should concentrate on
analyzing the 3T data only, and hopefully all of the subjects can be
rescanned on the 3T?  Thanks!

Jessica Liu

2011/6/23 Bruce Fischl 

> Hi Jessica,
>
> the 1.5t scan looks kind of washed out and low contrast, but of course it's
> hard to tell from an image. The 3T looks much crisper. Were the sequence
> parameters matched? I'm not sure what you're trying to show with this. The
> 3T multi-channel scan will have a much, much higher SNR than the 1.5T single
> channel, so the results will not at all be comparable.
>
>
> Bruce
>
>
> On Thu, 23 Jun 2011, Jessica Liu wrote:
>
>  Looking at the scans (attached, 3T on the left and 1.5T on the right,
>> yellow
>> hippocampus), I think you've made a good point.  More comments are much
>> appreciated, thanks!
>>
>> Jessica Liu
>>
>> 2011/6/23 Pedro Paulo de Magalhães Oliveira Junior 
>>  This is not normal. Maybe you should check the aseg volume for
>>  improper segmentation.
>>
>>
>> On Thu, Jun 23, 2011 at 19:27, Jessica Liu 
>> wrote:
>> Hi everyone!
>>
>> I'm currently a summer student working at a lab which uses
>> Freesurfer to measure hippocampal volumes.  I noticed that
>> scanning the same patient first on a GE 3T (Multi-channel head
>> coil) and then a GE 1.5T (single-channel head coil) 24 hours
>> later resulted in a 30% increase in the left hippocampus volume
>> and a 18% increase for the right hippocampus based on the values
>> in aseg.stats.  Can anyone please comment on this and explain
>> the large discrepancies?  Thanks!
>>
>> Jessica Liu
>>
>> __**_
>> 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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Re: [Freesurfer] Difference in hippocampal volume between scanners

[Bruce Fischl]

Hi Jessica,

the 1.5t scan looks kind of washed out and low contrast, but of course 
it's hard to tell from an image. The 3T looks much crisper. Were the 
sequence parameters matched? I'm not sure what you're trying to show with 
this. The 3T multi-channel scan will have a much, much higher SNR than the 
1.5T single channel, so the results will not at all be comparable.


Bruce


On Thu, 23 Jun 
2011, Jessica Liu wrote:



Looking at the scans (attached, 3T on the left and 1.5T on the right, yellow
hippocampus), I think you've made a good point.  More comments are much
appreciated, thanks!

Jessica Liu

2011/6/23 Pedro Paulo de Magalhães Oliveira Junior 
  This is not normal. Maybe you should check the aseg volume for
  improper segmentation.


On Thu, Jun 23, 2011 at 19:27, Jessica Liu 
wrote:
Hi everyone!

I'm currently a summer student working at a lab which uses
Freesurfer to measure hippocampal volumes.  I noticed that
scanning the same patient first on a GE 3T (Multi-channel head
coil) and then a GE 1.5T (single-channel head coil) 24 hours
later resulted in a 30% increase in the left hippocampus volume
and a 18% increase for the right hippocampus based on the values
in aseg.stats.  Can anyone please comment on this and explain
the large discrepancies?  Thanks!

Jessica Liu

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Re: [Freesurfer] Difference in hippocampal volume between scanners

[Bruce Fischl]

Hi Jessica,

what were the coils? Certainly you will find substantial differences 
comparing across both field strength and receive coil. Did the 
segmentations look reasonable? Was it the same sequence?


Bruce


On Thu, 23 Jun 2011, Jessica Liu wrote:


Hi everyone!

I'm currently a summer student working at a lab which uses Freesurfer to
measure hippocampal volumes.  I noticed that scanning the same patient first
on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head
coil) 24 hours later resulted in a 30% increase in the left hippocampus
volume and a 18% increase for the right hippocampus based on the values in
aseg.stats.  Can anyone please comment on this and explain the large
discrepancies?  Thanks!

Jessica Liu

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Re: [Freesurfer] Difference in hippocampal volume between scanners

[Pedro Paulo de Magalhães Oliveira Junior]

This is not normal. Maybe you should check the aseg volume for improper
segmentation.


On Thu, Jun 23, 2011 at 19:27, Jessica Liu  wrote:

> Hi everyone!
>
> I'm currently a summer student working at a lab which uses Freesurfer to
> measure hippocampal volumes.  I noticed that scanning the same patient first
> on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head
> coil) 24 hours later resulted in a 30% increase in the left hippocampus
> volume and a 18% increase for the right hippocampus based on the values in
> aseg.stats.  Can anyone please comment on this and explain the large
> discrepancies?  Thanks!
>
> Jessica Liu
>
> ___
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>
>
> 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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[Freesurfer] Difference in hippocampal volume between scanners

[Jessica Liu]

Hi everyone!

I'm currently a summer student working at a lab which uses Freesurfer to
measure hippocampal volumes.  I noticed that scanning the same patient first
on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head
coil) 24 hours later resulted in a 30% increase in the left hippocampus
volume and a 18% increase for the right hippocampus based on the values in
aseg.stats.  Can anyone please comment on this and explain the large
discrepancies?  Thanks!

Jessica Liu
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