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
Message: 6 Date: Tue, 10 Jan 2017 21:18:34 +0100 From: Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto: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 mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <9BCB373D-D368-4B36-B607-69E6A14AF952@nmr.mgh.harvard.edu mailto:9BCB373D-D368-4B36-B607-69E6A14AF952@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="us-ascii"
Hi Tamara,
mvoing in and popping out sounds like a scaling problem. We do only rigid transforms, so the scaling would already be in your original inputs. If that is the case, it could mean that there was a scanner calibration or something that caused scaled images and that would not be good. It should however appear in all images that have the calibration in between time points.
You can try to use mri_robust_register with the affine flag to see if any scaling is present in the rawavg.mgz images between the two time points (it should report scaling separately on the screen output), else use lta_diff with the appropriate flags. You can also look at the affininely registered images and see if it looks better.
Anyway if there is global scaling in the images, I would try to investigate a where this comes from and also drop that image from the study.
Best, Martin
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