Thanks Bruce,
Doing the bias correct and -odt float fixed the issue. Adding -odt short did not.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, 8 March 2016 11:46 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T2pial shrinks pial surface
it might, but you will need to make some fixes that are in 6.0 (soon) but not in 5.3. The 5.3 recon-all changes the T2 datatype to uchar when it resamples it to be in register with the T1. You should change that line to have -odt short or -odt float so that it doesn't saturate at 255, which is what caused the original problem.
On Tue, 8 Mar 2016, Chris Adamson wrote:
I see it now. I will try to perform a bias correction on the image prior to importing and see if that helps. Thanks Bruce.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, 8 March 2016 4:23 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T2pial shrinks pial surface
Hi Chris
I took a look, and the problem is that there are big changes in contrast between occipital and frontal lobes. If we normalize both posterior and frontal wm to 110, occipital gray matter gets mapped to 180 but frontal gray gets >255. This kind of thing can be caused by a transmit "bias" field, or by dielectric effects. I'm not sure why this is a problem with this dataset and not others
cheers Bruce
On Mon, 7 Mar 2016, Chris Adamson wrote:
Thanks Bruce.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson Sent: Monday, 7 March 2016 1:54 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T2pial shrinks pial surface
It is checkT2pial.zip
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 March 2016 1:35 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T2pial shrinks pial surface
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Mon, 7 Mar 2016, Chris Adamson wrote:
How can I upload it to you?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 March 2016 1:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T2pial shrinks pial surface
Hi Chris
if you upload that dataset I'll try to take a look soon
cheers Bruce
On Mon, 7 Mar 2016, Chris Adamson wrote:
The T2pial option mostly works beautifully. I have a few cases where the pial surface just shrinks globally and wraps over the white surface (see attached). I have checked the T2.mgz and the registration with the T1 is fine. This happens sometimes in one hemisphere only.
Any ideas?
[IMAGE]
Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Rd Parkville, Victoria 3052 AUS T: (03) 9936 6780 E: chris.adamson@mcri.edu.au www.mcri.edu.au
[IMAGE][IMAGE][IMAGE][IMAGE][IMAGE]
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