Re: [Freesurfer] longitudinal study

[Martin Reuter]

Hi Ken, 

you should always look at the output from the …long.base directories, those are 
the final outputs. Looks to me that you are looking at the cross sectional 
produced surfaces from the first stage. Those will be 
- in different spaces (as the heads are in different positions in the scanner)
- created independently and therefore will look more different from each other 
than the surfaces from the long stream.

Best, Martin

> On 25. Sep 2020, at 15:55, Douglas N. Greve  wrote:
> 
> What is your command line for visualization? Can you also show the base image 
> as an underlay?
> 
> On 9/24/2020 6:54 PM, KennethSPrice wrote:
>> External Email - Use Caution
>> 
>> Hello,
>> I am running a longitudinal study and am examining the pial surface for my 2 
>> timepoints. The surfaces are slightly offset. Will this effect my 
>> statistical analysis for volume and thickness? I have attached the pial 
>> surface for each time point to this email. Should I be examining 
>> timpoint1.long and timepoint2.long instead?
>> 
>> Thanks,
>> Ken
>> 
>> 
>> Sent with ProtonMail  Secure Email.
>> 
>> 
>> 
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Re: [Freesurfer] longitudinal study

[Douglas N. Greve]

What is your command line for visualization? Can you also show the base 
image as an underlay?


On 9/24/2020 6:54 PM, KennethSPrice wrote:


External Email - Use Caution

Hello,
I am running a longitudinal study and am examining the pial surface 
for my 2 timepoints. The surfaces are slightly offset. Will this 
effect my statistical analysis for volume and thickness? I have 
attached the pial surface for each time point to this email. Should I 
be examining timpoint1.long and timepoint2.long instead?


Thanks,
Ken


Sent with ProtonMail  Secure Email.


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[Freesurfer] longitudinal study

[KennethSPrice]

External Email - Use Caution

Hello,
I am running a longitudinal study and am examining the pial surface for my 2 
timepoints. The surfaces are slightly offset. Will this effect my statistical 
analysis for volume and thickness? I have attached the pial surface for each 
time point to this email. Should I be examining timpoint1.long and 
timepoint2.long instead?

Thanks,
Ken

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[Freesurfer] Longitudinal study dimension mismatch

[KennethSPrice]

External Email - Use Caution

Hello Freesurfers!

I am running a recon-all -long study and one of my subjects is giving me 
trouble. The brain segmentation volume for tp2 is greater than tp1.  The scans 
were taken from the same machine with the same parameters, but the dimensions 
are mismatched:

Volumes differ in dimension
v1dim 512 512 32 1
v2dim 560 560 30 1

I am worried that dimension mismatch is causing an error in brain volume 
estimation. I have tried reslicing v1 to v2 dimensions but freesurfer did not 
like it. Would a dimension mismatch lead to significant volume differences, and 
is there any work around? \

Thanks,
Ken

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Re: [Freesurfer] Longitudinal study dimension mismatch

[Tim Schäfer]

External Email - Use Caution

The data will be resampled by FreeSurfer, so as far as I know it should not 
make a difference as far as FreeSurfer is concerned.

But if you expect the two subjects to have the same dimensions, and that is not 
true, I would still check why that is the case.

Tim

> On May 30, 2020 at 9:05 PM KennethSPrice  wrote:
> 
> 
> External Email - Use Caution
> 
> Hello Freesurfers!
> 
> I am running a recon-all -long study and one of my subjects is giving me 
> trouble. The brain segmentation volume for tp2 is greater than tp1.  The 
> scans were taken from the same machine with the same parameters, but the 
> dimensions are mismatched:
> 
> Volumes differ in dimension
> v1dim 512 512 32 1
> v2dim 560 560 30 1
> 
> I am worried that dimension mismatch is causing an error in brain volume 
> estimation. I have tried reslicing v1 to v2 dimensions but freesurfer did not 
> like it. Would a dimension mismatch lead to significant volume differences, 
> and is there any work around? \
> 
> Thanks,
> Ken
> 
> Sent with [ProtonMail](https://protonmail.com) Secure 
> Email.___
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-- 
Tim Schäfer

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Re: [Freesurfer] Longitudinal study concept question

[Martin Reuter]

Hi Gregory,

If looking at longitudinal changes, I would use uncorrected ROI 
volumes.  You could consider including ICV as a covariate (for offset 
and slope interaction, to test if ICV has an effect on your slopes).


Best, Martin


On 05/19/2017 04:44 PM, Gregory Book wrote:
In writing a paper of longitudinal changes in a large heterogeneous 
population with no group comparisons, what would be considered "more 
important" to include: absolute ROI volumes, or volumes corrected for 
ICV?


Using ICV corrected volumes makes sense when comparing groups, but 
when just describing population changes over time, for example a cross 
section of a population over a lifespan, is it better to use absolute 
volumes, corrected volumes, or both?



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[Freesurfer] Longitudinal study concept question

[Gregory Book]

In writing a paper of longitudinal changes in a large heterogeneous
population with no group comparisons, what would be considered "more
important" to include: absolute ROI volumes, or volumes corrected for ICV?

Using ICV corrected volumes makes sense when comparing groups, but when
just describing population changes over time, for example a cross section
of a population over a lifespan, is it better to use absolute volumes,
corrected volumes, or both?
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Re: [Freesurfer] Longitudinal study: analyze results

[Martin Reuter]

Hi Gonzalo,

yes, exactly, you only look at the *.long.* folders. Take a look at this 
page:


http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics
specifically if you have 2 time points for all subjects, you can use the 
tools for analyzing slopes:

http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel


Cheers, Martin

On 05/27/2015 10:29 AM, Gonzalo Rojas Costa wrote:


Hi:

For example: if I want to compare the volume of left hyppocampus in 
two time points, could I compare the volume in aseg.stats file of both 
"long" folders?...


Sincerely,

Gonzalo Rojas Costa


Gonzalo Rojas Costa
Advanced Medical Image Processing Laboratory
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl 



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--
Dr. Martin Reuter

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
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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[Freesurfer] Longitudinal study: analyze results

[Gonzalo Rojas Costa]

Hi:

For example: if I want to compare the volume of left hyppocampus in two
time points, could I compare the volume in aseg.stats file of both "long"
folders?...

Sincerely,

Gonzalo Rojas Costa


Gonzalo Rojas Costa
Advanced Medical Image Processing Laboratory
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
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[Freesurfer] Longitudinal study... analyze of results....

[Gonzalo Rojas Costa]

Hi:

I want to do a longitudinal study between two time points of a patient... I
want to compare the volume of the hypocampii, white matter, etc... I did
the computation of both time points, I created the "base" image, and the
"long" ones... How can I analyze the aseg.stats files in each "long" folder
?...

Sincerely,

Gonzalo Rojas Costa


Gonzalo Rojas Costa
Advanced Medical Image Processing Laboratory
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
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Re: [Freesurfer] longitudinal study in counterbalance design

[Douglas N Greve]

In terms of just giving it a name, it should not matter since all of the
time points are treated equally in the longitudinal stream. When you go
to analyze it, the order will make a difference (and I assume you'll use
phase).
doug

On 05/07/2012 11:59 PM, lordowen wrote:
> Hi all:
>
> We performed a thickness change study which related to the menstrual
> cycle. We scanned subjects during different menstrual phases in a
> counterbalance manner. Thus when we conduct a longitudinal analysis,
> we need to set time point according to the actual scanning order
> (i.e., 1st scan as Tp1 and so on) or according to the phase (i.e.,
> menstruation phase as Tp1 and other phase as TpN)?
>
> Thanks for your suggestion.
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] longitudinal study in counterbalance design

[Martin Reuter]

Hi, 
I'd recommend to use time for the order when processing. The order of time 
points is not relevant in the longitudinal stream but this way the design is 
more balanced.

Best Martin

On May 7, 2012, at 23:59, lordowen  wrote:

> Hi all:
> 
> We performed a thickness change study which related to the menstrual
> cycle. We scanned subjects during different menstrual phases in a
> counterbalance manner. Thus when we conduct a longitudinal analysis,
> we need to set time point according to the actual scanning order
> (i.e., 1st scan as Tp1 and so on) or according to the phase (i.e.,
> menstruation phase as Tp1 and other phase as TpN)?
> 
> Thanks for your suggestion.
> 
> -- 
> Best regards
> --
> 杜政昊
> 
> Cheng-Hao Tu, PhD
> Post Doctoral Research Fellow
> Integrated Brain Research Unit
> Department of Medical Research and Education
> Taipei Veterans General Hospital
> No.201, Sect.2, Shih-Pai Rd.
> Taipei
> Taiwan
> Email: lordo...@ms10.hinet.net or lordowe...@gmail.com
> Tel: +886-2-28712121 ext 3474
> Fax: +886-2-28745182
> 
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[Freesurfer] longitudinal study in counterbalance design

[lordowen]

Hi all:

We performed a thickness change study which related to the menstrual
cycle. We scanned subjects during different menstrual phases in a
counterbalance manner. Thus when we conduct a longitudinal analysis,
we need to set time point according to the actual scanning order
(i.e., 1st scan as Tp1 and so on) or according to the phase (i.e.,
menstruation phase as Tp1 and other phase as TpN)?

Thanks for your suggestion.

-- 
Best regards
--
杜政昊

Cheng-Hao Tu, PhD
Post Doctoral Research Fellow
Integrated Brain Research Unit
Department of Medical Research and Education
Taipei Veterans General Hospital
No.201, Sect.2, Shih-Pai Rd.
Taipei
Taiwan
Email: lordo...@ms10.hinet.net or lordowe...@gmail.com
Tel: +886-2-28712121 ext 3474
Fax: +886-2-28745182

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Re: [Freesurfer] longitudinal study

[Nick Schmansky]

Guang,

See this page for details:

http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

(yes, you will need to process all subjects using the default
cross-sectional stream).

Nick


On Wed, 2009-09-16 at 11:54 -0500, Guang Zeng wrote:
> Hi, there,
> 
> I am going to run the FreeSurfer Longitudinal Stream (FS 4.5) on data
> from different timepoints.
> Do we need cross-sectionally process all time points with the default
> workflow, or just need run the first step 
> of the default workflow. 
> 
> 
> Thanks a lot!
> Guang
> 
> 
> 
> 
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[Freesurfer] longitudinal study

[Guang Zeng]

Hi, there,

I am going to run the FreeSurfer Longitudinal Stream (FS 4.5) on data from 
different timepoints.
Do we need cross-sectionally process all time points with the default workflow, 
or just need run the first step 
of the default workflow. 


Thanks a lot!
Guang



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Re: [Freesurfer] longitudinal study

[Bruce Fischl]

Hi Linda,

we haven't found any problems in that age range. Down to 3 years old is 
probably fine, although if you were scanning that young there might be 
some things we would advise. 1l years old is no problem though.


cheers,
Bruce

On Tue, 13 Nov 2007, Linda.E Campbell wrote:


Hi,
I am about to start processing some longitudinal data and am looking for
appropriate software. I know the Freesurfer allows for longitudinal
designs but how appropriate is it to use for developing brains, ie in my
sample the subjects are adolescents between 14-20 and they were last
scanned three years ago. Since the brain and skull size changes in that
time would Freesurfer be able to take that into account and what would
be the best way to go about it. I would be most grateful for your
advice.

Thank you

Linda


Dr. Linda Campbell, PhD
NH&MRC Research fellow & Project Manager
University of Newcastle Priority Research Centre
Brain & Mental Health

Affiliations:
Hunter Medical Research Institute (HMRI)
Neuroscience Institute of Schizophrenia
and Allied Disorders (NISAD)

Mail to:

Centre for Brain & Mental Health Research
Officers Quarters Complex
James Fletcher Hospital
Newcomen Street
Newcastle NSW 2300
Australia

Ph: +61-2 4924 6648
Fax: +61-2 4924 6608
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[Freesurfer] longitudinal study

[Linda.E Campbell]

Hi,
I am about to start processing some longitudinal data and am looking for
appropriate software. I know the Freesurfer allows for longitudinal
designs but how appropriate is it to use for developing brains, ie in my
sample the subjects are adolescents between 14-20 and they were last
scanned three years ago. Since the brain and skull size changes in that
time would Freesurfer be able to take that into account and what would
be the best way to go about it. I would be most grateful for your
advice.

Thank you

Linda


Dr. Linda Campbell, PhD
NH&MRC Research fellow & Project Manager
University of Newcastle Priority Research Centre 
Brain & Mental Health

Affiliations:
Hunter Medical Research Institute (HMRI)
Neuroscience Institute of Schizophrenia
and Allied Disorders (NISAD)

Mail to:

Centre for Brain & Mental Health Research
Officers Quarters Complex
James Fletcher Hospital
Newcomen Street
Newcastle NSW 2300
Australia

Ph: +61-2 4924 6648
Fax: +61-2 4924 6608
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