Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream
Hi Dr. Reuter,
Thank you for the clarification.
The differences I am seeing are also in the T1.mgz file in the longitudinal run folder. I assume it is okay to use the T1.mgz from the longitudinal outputs as the original image as I can easily compare the same slice across different time points?
Also, on a related note, I have two scans (time 1 and time 2) that doesn't seem to align perfectly with the template or with each other. When I use the opacity slider to transition from the template to time 1 it looks like the brain is 'moving in'. When I transition from template to time 2 the brain seems to 'pop out'. Similarly, when I transition from time 1 to time 2, it looks like the brain is popping out. With my other images, there is a smooth transition from time 1 to time 2 and a relatively smooth transition from the template to the time points. Do you think this is problematic?
Thank you again for your help.
Best, Tamara
Message: 4 Date: Wed, 28 Dec 2016 11:20:36 +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: F2352B06-D00A-409A-9FB3-7AE1FD6EA20B@nmr.mgh.harvard.edu Content-Type: text/plain; charset=us-ascii
Hi Tamara,
three out of how many? I would probably remove those three as whatever you measure in them could be driven by the acquisition differences, but it depends on what acquisition differences you have. If it is only small differences, like tiny deviations in the voxel size etc, it should be OK.
I have no idea where the other intensity differences could come from. If you see them in the original inputs, maybe an MR physicist could take a look and advise. If you have a concrete case where the inputs are OK, but you think that in FS processed images show different contrast or intensities, I would need to have those images to see if I can replicate that.
Best, Martin
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
On 09 Jan 2017, at 17:24, Tamara Tavares ttavare@uwo.ca wrote:
Hi Dr. Reuter,
Thank you for the clarification.
The differences I am seeing are also in the T1.mgz file in the longitudinal run folder. I assume it is okay to use the T1.mgz from the longitudinal outputs as the original image as I can easily compare the same slice across different time points?
Also, on a related note, I have two scans (time 1 and time 2) that doesn't seem to align perfectly with the template or with each other. When I use the opacity slider to transition from the template to time 1 it looks like the brain is 'moving in'. When I transition from template to time 2 the brain seems to 'pop out'. Similarly, when I transition from time 1 to time 2, it looks like the brain is popping out. With my other images, there is a smooth transition from time 1 to time 2 and a relatively smooth transition from the template to the time points. Do you think this is problematic?
Thank you again for your help.
Best, Tamara
Message: 4 Date: Wed, 28 Dec 2016 11:20:36 +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: <F2352B06-D00A-409A-9FB3-7AE1FD6EA20B@nmr.mgh.harvard.edu mailto:F2352B06-D00A-409A-9FB3-7AE1FD6EA20B@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=us-ascii
Hi Tamara,
three out of how many? I would probably remove those three as whatever you measure in them could be driven by the acquisition differences, but it depends on what acquisition differences you have. If it is only small differences, like tiny deviations in the voxel size etc, it should be OK.
I have no idea where the other intensity differences could come from. If you see them in the original inputs, maybe an MR physicist could take a look and advise. If you have a concrete case where the inputs are OK, but you think that in FS processed images show different contrast or intensities, I would need to have those images to see if I can replicate that.
Best, Martin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Tamara Tavares