Hi Martin,

Thank you for the clarification. I assume this participant should be removed? As a rule of thumb, should I exclude participants who have a total of 3% scaling? Is there a way to check potential scaling problems (e.g. looking into the recon-all.log to see scaling or checking alignment between the longitudinal time points)?

Thank you again for your help.

Best,

Tamara

Message: 7
Date: Thu, 12 Jan 2017 16:20:11 +0100
From: Martin Reuter <mreuter@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Brighter image at baseline vs. follow up
using longitudinal processing stream
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2D4D7B7C-9915-454C-9A41-AA9FDE9D3C46@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"

Hi Tamara,

that information is in the screen output:

Determinant : 1.03358

also
Scale = diag([ 1.0109774487584 1.0113715685396 1.0108915357302 ])

so it finds some scaling (approx 1% in each axis direction, so a total of 3%). This can happen in individual cases, but if it is consistent I would be worried.

Best, Martin

> On 11 Jan 2017, at 21:21, Tamara Tavares <ttavare@uwo.ca> wrote:
>
> Hi Dr. Reuter.
>
> Thank you again for your help.
>
> I ran the following command: "mri_robust_register --mov rawavg_1.mgz --dst rawavg_2.mgz --lta v1to2.lta --affine --satit" on the two rawavg.mgz images; one from each time point from the cross-sectional outputs. I have attached the information from the terminal and the output. Are these outputs appropriate to find the scaling information? If so, where can I find it? I am not very familiar with transformations, thus any information or directions to resources I can use would be very much appreciated.
>
> Thank you in advance for you help.
>
> Best,
> Tamara