Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

[Pradeep]

Thanks you for the reply.

Martin, the scans are 0,14 and 21 days a part.
I will run a few more subjects and check the results as you suggested.

On Fri, Apr 17, 2015 at 8:59 AM, Bruce Fischl 
wrote:

> you should also plot them on the same axes (or at the very least with the
> same limits)
>
> On Fri, 17 Apr 2015, Martin Reuter wrote:
>
>  Hi Pradeep,
>>
>> is this the result of a single subject? In a single subject lot's of
>> things
>> can happen (e.g. motion artefacts can affect a single time point, other
>> imaging or measurement noise will have effects). Also how far are the time
>> points apart? Run the same thing with 20 subjects and you should see
>> significantly reduced variablility in the longitudinal stream vs the cross
>> sectional one.
>>
>> Best, Martin
>>
>> On 04/16/2015 01:12 PM, Pradeep wrote:
>>   Hello All,
>> I have pre-processed a subject that has T1 scans at 3 time points
>> using the freesurfer cross-sectional and longitudinal methods. The
>> results show a lot of variability. I have attached the plots. Any
>> advice would be much appreciated.
>> Thanks,
>> Pradeep
>>
>> On Wed, Apr 15, 2015 at 5:26 PM, Pradeep  wrote:
>>   Hello All,
>> I have pre-processed a subject that has T1 scans at 3 time using
>> the freesurfer cross-sectional and longitudinal methods. The
>> results show a lot of variability. I have attached the plots.
>> Any advice would be much appreciated.
>> Thanks,
>> Pradeep
>>
>> On Wed, Jun 4, 2014 at 12:03 PM, Alexandru Hanganu
>>  wrote:
>>   Thank you very much for your answer Bruce !
>>
>>   have a nice evening,
>>
>>   Alex.
>>
>>
>>   Le 3 juin 14 7:6, Bruce Fischl a écrit :
>>   > Hi Alex
>>   >
>>   > I would think that longitudinal analysis is still
>>   the way to go as we try
>>   > to improve both reliability and sensitivity using
>>   the fact that we have
>>   > multiple scans/subject.
>>   >
>>   > cheers
>>   > Bruce
>>   > On Tue, 3 Jun 2014, Alexandru Hanganu wrote:
>>   >
>>   >> Hello Everyone,
>>   >>
>>   >> could someone please give us an advice about
>>   which method you consider is
>>   >> the best for our study ?
>>   >>
>>   >> we have two groups with MRI at Time 1. Each group
>>   received medication. After
>>   >> this we performed another MRI at Time 2 after 2
>>   weeks.
>>   >>
>>   >> The best method for this study is a longitudinal
>>   one or a cross-sectional
>>   >> GLM ?
>>   >>
>>   >> We consider that the distance between the time
>>   points is too small, and the
>>   >> longitudinal method is not the best choice.
>>   Hence, this study should be
>>   >> treated as a cross-sectional one. In this case we
>>   think about performing a
>>   >> simple GLM with the contrasts:
>>   >> 0.5 0.5 0.5 0.5
>>   >> or 1 -1 -1 1
>>   >>
>>   >> for the groups:
>>   >> 1) grp 1 time 1
>>   >> 2) grp 1 time 2
>>   >> 3) grp 2 time 1
>>   >> 4) grp 2 time 2
>>   >>
>>   >> we are searching to see whether medication had
>>   any impact on the cortical
>>   >> morphology in each group and between the groups.
>>   >>
>>   >> Thank you !
>>   >> Best regards,
>>   >> Alex.
>>   >>
>>   >>
>>   > ___
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>>   >
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>>   > addressed. If you believe this e-mail was sent to
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>>
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Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

[Bruce Fischl]

you should also plot them on the same axes (or at the very least with the 
same limits)

On Fri, 17 Apr 2015, Martin Reuter wrote:


Hi Pradeep,

is this the result of a single subject? In a single subject lot's of things
can happen (e.g. motion artefacts can affect a single time point, other
imaging or measurement noise will have effects). Also how far are the time
points apart? Run the same thing with 20 subjects and you should see
significantly reduced variablility in the longitudinal stream vs the cross
sectional one.

Best, Martin

On 04/16/2015 01:12 PM, Pradeep wrote:
  Hello All, 
I have pre-processed a subject that has T1 scans at 3 time points
using the freesurfer cross-sectional and longitudinal methods. The
results show a lot of variability. I have attached the plots. Any
advice would be much appreciated. 
Thanks,
Pradeep

On Wed, Apr 15, 2015 at 5:26 PM, Pradeep  wrote:
  Hello All, 
I have pre-processed a subject that has T1 scans at 3 time using
the freesurfer cross-sectional and longitudinal methods. The
results show a lot of variability. I have attached the plots.
Any advice would be much appreciated. 
Thanks,
Pradeep

On Wed, Jun 4, 2014 at 12:03 PM, Alexandru Hanganu
 wrote:
  Thank you very much for your answer Bruce !

  have a nice evening,

  Alex.


  Le 3 juin 14 7:6, Bruce Fischl a écrit :
  > Hi Alex
  >
  > I would think that longitudinal analysis is still
  the way to go as we try
  > to improve both reliability and sensitivity using
  the fact that we have
  > multiple scans/subject.
  >
  > cheers
  > Bruce
  > On Tue, 3 Jun 2014, Alexandru Hanganu wrote:
  >
  >> Hello Everyone,
  >>
  >> could someone please give us an advice about
  which method you consider is
  >> the best for our study ?
  >>
  >> we have two groups with MRI at Time 1. Each group
  received medication. After
  >> this we performed another MRI at Time 2 after 2
  weeks.
  >>
  >> The best method for this study is a longitudinal
  one or a cross-sectional
  >> GLM ?
  >>
  >> We consider that the distance between the time
  points is too small, and the
  >> longitudinal method is not the best choice.
  Hence, this study should be
  >> treated as a cross-sectional one. In this case we
  think about performing a
  >> simple GLM with the contrasts:
  >> 0.5 0.5 0.5 0.5
  >> or 1 -1 -1 1
  >>
  >> for the groups:
  >> 1) grp 1 time 1
  >> 2) grp 1 time 2
  >> 3) grp 2 time 1
  >> 4) grp 2 time 2
  >>
  >> we are searching to see whether medication had
  any impact on the cortical
  >> morphology in each group and between the groups.
  >>
  >> Thank you !
  >> Best regards,
  >> Alex.
  >>
  >>
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Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

[Martin Reuter]

Hi Pradeep,

is this the result of a single subject? In a single subject lot's of 
things can happen (e.g. motion artefacts can affect a single time point, 
other imaging or measurement noise will have effects). Also how far are 
the time points apart? Run the same thing with 20 subjects and you 
should see significantly reduced variablility in the longitudinal stream 
vs the cross sectional one.


Best, Martin

On 04/16/2015 01:12 PM, Pradeep wrote:

Hello All,

I have pre-processed a subject that has T1 scans at 3 time points 
using the freesurfer cross-sectional and longitudinal methods. The 
results show a lot of variability. I have attached the plots. Any 
advice would be much appreciated.


Thanks,
Pradeep

On Wed, Apr 15, 2015 at 5:26 PM, Pradeep > wrote:


Hello All,

I have pre-processed a subject that has T1 scans at 3 time using
the freesurfer cross-sectional and longitudinal methods. The
results show a lot of variability. I have attached the plots. Any
advice would be much appreciated.

Thanks,
Pradeep

On Wed, Jun 4, 2014 at 12:03 PM, Alexandru Hanganu
mailto:al.hang...@yahoo.ca>> wrote:

Thank you very much for your answer Bruce !

have a nice evening,

Alex.


Le 3 juin 14 7:6, Bruce Fischl a écrit :
> Hi Alex
>
> I would think that longitudinal analysis is still the way to
go as we try
> to improve both reliability and sensitivity using the fact
that we have
> multiple scans/subject.
>
> cheers
> Bruce
> On Tue, 3 Jun 2014, Alexandru Hanganu wrote:
>
>> Hello Everyone,
>>
>> could someone please give us an advice about which method
you consider is
>> the best for our study ?
>>
>> we have two groups with MRI at Time 1. Each group received
medication. After
>> this we performed another MRI at Time 2 after 2 weeks.
>>
>> The best method for this study is a longitudinal one or a
cross-sectional
>> GLM ?
>>
>> We consider that the distance between the time points is
too small, and the
>> longitudinal method is not the best choice. Hence, this
study should be
>> treated as a cross-sectional one. In this case we think
about performing a
>> simple GLM with the contrasts:
>> 0.5 0.5 0.5 0.5
>> or 1 -1 -1 1
>>
>> for the groups:
>> 1) grp 1 time 1
>> 2) grp 1 time 2
>> 3) grp 2 time 1
>> 4) grp 2 time 2
>>
>> we are searching to see whether medication had any impact
on the cortical
>> morphology in each group and between the groups.
>>
>> Thank you !
>> Best regards,
>> Alex.
>>
>>
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--
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Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
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Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

[Pradeep]

Hello All,

I have pre-processed a subject that has T1 scans at 3 time points using the
freesurfer cross-sectional and longitudinal methods. The results show a lot
of variability. I have attached the plots. Any advice would be much
appreciated.

Thanks,
Pradeep

On Wed, Apr 15, 2015 at 5:26 PM, Pradeep  wrote:

> Hello All,
>
> I have pre-processed a subject that has T1 scans at 3 time using the
> freesurfer cross-sectional and longitudinal methods. The results show a lot
> of variability. I have attached the plots. Any advice would be much
> appreciated.
>
> Thanks,
> Pradeep
>
> On Wed, Jun 4, 2014 at 12:03 PM, Alexandru Hanganu 
> wrote:
>
>> Thank you very much for your answer Bruce !
>>
>> have a nice evening,
>>
>> Alex.
>>
>>
>> Le 3 juin 14 7:6, Bruce Fischl a écrit :
>> > Hi Alex
>> >
>> > I would think that longitudinal analysis is still the way to go as we
>> try
>> > to improve both reliability and sensitivity using the fact that we have
>> > multiple scans/subject.
>> >
>> > cheers
>> > Bruce
>> > On Tue, 3 Jun 2014, Alexandru Hanganu wrote:
>> >
>> >> Hello Everyone,
>> >>
>> >> could someone please give us an advice about which method you consider
>> is
>> >> the best for our study ?
>> >>
>> >> we have two groups with MRI at Time 1. Each group received medication.
>> After
>> >> this we performed another MRI at Time 2 after 2 weeks.
>> >>
>> >> The best method for this study is a longitudinal one or a
>> cross-sectional
>> >> GLM ?
>> >>
>> >> We consider that the distance between the time points is too small,
>> and the
>> >> longitudinal method is not the best choice. Hence, this study should be
>> >> treated as a cross-sectional one. In this case we think about
>> performing a
>> >> simple GLM with the contrasts:
>> >> 0.5 0.5 0.5 0.5
>> >> or 1 -1 -1 1
>> >>
>> >> for the groups:
>> >> 1) grp 1 time 1
>> >> 2) grp 1 time 2
>> >> 3) grp 2 time 1
>> >> 4) grp 2 time 2
>> >>
>> >> we are searching to see whether medication had any impact on the
>> cortical
>> >> morphology in each group and between the groups.
>> >>
>> >> Thank you !
>> >> Best regards,
>> >> Alex.
>> >>
>> >>
>> > ___
>> > 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] Advice - best method, longitudinal vs. cross-sectional

[Alexandru Hanganu]

Thank you very much for your answer Bruce !

have a nice evening,

Alex.


Le 3 juin 14 7:6, Bruce Fischl a écrit :
> Hi Alex
>
> I would think that longitudinal analysis is still the way to go as we try
> to improve both reliability and sensitivity using the fact that we have
> multiple scans/subject.
>
> cheers
> Bruce
> On Tue, 3 Jun 2014, Alexandru Hanganu wrote:
>
>> Hello Everyone,
>>
>> could someone please give us an advice about which method you consider is
>> the best for our study ?
>>
>> we have two groups with MRI at Time 1. Each group received medication. After
>> this we performed another MRI at Time 2 after 2 weeks.
>>
>> The best method for this study is a longitudinal one or a cross-sectional
>> GLM ?
>>
>> We consider that the distance between the time points is too small, and the
>> longitudinal method is not the best choice. Hence, this study should be
>> treated as a cross-sectional one. In this case we think about performing a
>> simple GLM with the contrasts:
>> 0.5 0.5 0.5 0.5
>> or 1 -1 -1 1
>>
>> for the groups:
>> 1) grp 1 time 1
>> 2) grp 1 time 2
>> 3) grp 2 time 1
>> 4) grp 2 time 2
>>
>> we are searching to see whether medication had any impact on the cortical
>> morphology in each group and between the groups.
>>
>> Thank you !
>> Best regards,
>> Alex.
>>
>>
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Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

[Martin Reuter]

Hi Alex,
The time distance does not matter. It's best to use a longitudinal method (both 
for the image processing, to reduce noise, and for the statistics, to gain 
power).

 Your design seems to be missing a control group (unless one off your groups is 
placebo). In your design you can compare changes across the two groups. But if 
you look at a single group and detect longitudinal change you will not know if 
it is the drug or something else that caused it. 


Best Martin

Sent via my smartphone, please excuse brevity.

 Original message 
From: Alexandru Hanganu  
Date:06/03/2014  6:15 PM  (GMT-05:00) 
To: FS Mailing List  
Subject: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional 

Hello Everyone,

could someone please give us an advice about which method you consider is the 
best for our study ?

we have two groups with MRI at Time 1. Each group received medication. After 
this we performed another MRI at Time 2 after 2 weeks.

The best method for this study is a longitudinal one or a cross-sectional GLM ?

We consider that the distance between the time points is too small, and the 
longitudinal method is not the best choice. Hence, this study should be treated 
as a cross-sectional one. In this case we think about performing a simple GLM 
with the contrasts:
0.5 0.5 0.5 0.5
or 1 -1 -1 1

for the groups:
1) grp 1 time 1
2) grp 1 time 2
3) grp 2 time 1
4) grp 2 time 2

we are searching to see whether medication had any impact on the cortical 
morphology in each group and between the groups.

Thank you !
Best regards,
Alex.
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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
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Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

[Bruce Fischl]

Hi Alex

I would think that longitudinal analysis is still the way to go as we try 
to improve both reliability and sensitivity using the fact that we have 
multiple scans/subject.

cheers
Bruce
On Tue, 3 Jun 2014, Alexandru Hanganu wrote:

> Hello Everyone,
> 
> could someone please give us an advice about which method you consider is
> the best for our study ?
> 
> we have two groups with MRI at Time 1. Each group received medication. After
> this we performed another MRI at Time 2 after 2 weeks.
> 
> The best method for this study is a longitudinal one or a cross-sectional
> GLM ?
> 
> We consider that the distance between the time points is too small, and the
> longitudinal method is not the best choice. Hence, this study should be
> treated as a cross-sectional one. In this case we think about performing a
> simple GLM with the contrasts:
> 0.5 0.5 0.5 0.5
> or 1 -1 -1 1
> 
> for the groups:
> 1) grp 1 time 1
> 2) grp 1 time 2
> 3) grp 2 time 1
> 4) grp 2 time 2
> 
> we are searching to see whether medication had any impact on the cortical
> morphology in each group and between the groups.
> 
> Thank you !
> Best regards,
> Alex.
> 
>
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[Freesurfer] Advice - best method, longitudinal vs. cross-sectional

[Alexandru Hanganu]

Hello Everyone,

could someone please give us an advice about which method you consider 
is the best for our study ?


we have two groups with MRI at Time 1. Each group received medication. 
After this we performed another MRI at Time 2 after 2 weeks.


The best method for this study is a longitudinal one or a 
cross-sectional GLM ?


We consider that the distance between the time points is too small, and 
the longitudinal method is not the best choice. Hence,this study should 
be treated as a cross-sectional one. In this case we think about 
performing a simple GLM with the contrasts:

0.5 0.5 0.5 0.5
or 1 -1 -1 1

for the groups:
1) grp 1 time 1
2) grp 1 time 2
3) grp 2 time 1
4) grp 2 time 2

we are searching to see whether medication had any impact on the 
cortical morphology in each group and between the groups.


Thank you !
Best regards,
Alex.
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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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