Re: [Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies

2018-09-05 Thread Daniel Ferreira 
External Email - Use Caution

Hi Martin,

Thank you very much for your answer.

Best regards

Dani

2018-09-04 16:38 GMT+02:00 Martin Reuter :

> Hi Dani,
>
> the regular FreeSurfer stream samples everything to 1mm isotropic. This is
> of course problematic, if you have one group scanned at 1mm and the other
> at a different resolution (as group differences could be affected by the
> different resolutions). You would never know how much of what you get is
> group and how much is resolution.
>
> Similarly this is problematic if you switch scanner, software, head-coil,
> resolution in a longitudinal study. Effects cannot be separated any longer
> and all you can report in a paper is that what you find is longitudinal
> effect plus resolution effects and you don’t know how much is which.
>
> FreeSurfers longitudinal stream therefore requires inputs to be the same
> resolution. This safety feature (to prevent potentially meaningless
> analysis) can be circumvented by manually sampling images first - at your
> own risk. If you go that way, you should at least also interpolate the 1mm
> images to a new position (at least then both images will have interpolation
> artefacts, so that differences are only the acquisition resolution and not
> additionally interpolation artefacts in one of the time points).
>
> As an example, taking the same image twice, mapping one to a different
> location and back again produces interpolation artefacts that are
> significant and at orders comparable with 1 year of neurodegenerative
> disease.
>
> Best, Martin
>
>
>
>
>
> On 30. Aug 2018, at 18:22, Daniel Ferreira  wrote:
>
>
>
> Dear colleagues,
>
> I was wondering if resampling voxel size is done during recon-all.
>
> Also, I have data with voxel resolution of 1x1x1 mm at baseline and
> 1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation
> by default (or can be performed by any way) that minimizes these
> differences in somehow.
>
> Thank you very much
>
> Dani
>
> --
>
> *Daniel Ferreira, PhD, Assistant Professor*
>
> Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences
> and Society
>
> Karolinska Institutet (Sweden)
>
> *Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 |
> email: daniel.ferreira.padi...@ki.se *
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-- 

*Daniel Ferreira, PhD, Assistant Professor*

Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences
and Society

Karolinska Institutet (Sweden)

*Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 |
email: daniel.ferreira.padi...@ki.se *
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Re: [Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies

2018-09-04 Thread Martin Reuter 
Hi Dani, 

the regular FreeSurfer stream samples everything to 1mm isotropic. This is of 
course problematic, if you have one group scanned at 1mm and the other at a 
different resolution (as group differences could be affected by the different 
resolutions). You would never know how much of what you get is group and how 
much is resolution. 

Similarly this is problematic if you switch scanner, software, head-coil, 
resolution in a longitudinal study. Effects cannot be separated any longer and 
all you can report in a paper is that what you find is longitudinal effect plus 
resolution effects and you don’t know how much is which. 

FreeSurfers longitudinal stream therefore requires inputs to be the same 
resolution. This safety feature (to prevent potentially meaningless analysis) 
can be circumvented by manually sampling images first - at your own risk. If 
you go that way, you should at least also interpolate the 1mm images to a new 
position (at least then both images will have interpolation artefacts, so that 
differences are only the acquisition resolution and not additionally 
interpolation artefacts in one of the time points). 

As an example, taking the same image twice, mapping one to a different location 
and back again produces interpolation artefacts that are significant and at 
orders comparable with 1 year of neurodegenerative disease. 

Best, Martin





> On 30. Aug 2018, at 18:22, Daniel Ferreira  wrote:
> 
> 
> 
> 
> Dear colleagues,
> 
> I was wondering if resampling voxel size is done during recon-all.
> 
> Also, I have data with voxel resolution of 1x1x1 mm at baseline and 
> 1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation 
> by default (or can be performed by any way) that minimizes these differences 
> in somehow.
> 
> Thank you very much
> 
> Dani
> 
> -- 
> Daniel Ferreira, PhD, Assistant Professor
> 
> Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences 
> and Society
> 
> Karolinska Institutet (Sweden)
> 
> Address: Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: 
> daniel.ferreira.padi...@ki.se 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies

2018-08-30 Thread Daniel Ferreira 
External Email - Use Caution

Dear colleagues,

I was wondering if resampling voxel size is done during recon-all.

Also, I have data with voxel resolution of 1x1x1 mm at baseline and
1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation
by default (or can be performed by any way) that minimizes these
differences in somehow.

Thank you very much

Dani

-- 

*Daniel Ferreira, PhD, Assistant Professor*

Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences
and Society

Karolinska Institutet (Sweden)

*Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 |
email: daniel.ferreira.padi...@ki.se *
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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 error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.