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 <ttav...@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 <mreu...@nmr.mgh.harvard.edu > <mailto:mreu...@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-b607-69e6a14af...@nmr.mgh.harvard.edu > <mailto:9bcb373d-d368-4b36-b607-69e6a14af...@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 > > > <terminal_output_mri_robustcommand.txt><v1to2.ita.txt>_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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