Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-20 Thread Martijn Steenwijk
] T2pial/FLAIRpial processing issues Hi Matt, Bruce, The problems are indeed a flirt issue, but given that it's programmed with --init-fsl there is not much flexibility

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-15 Thread Martijn Steenwijk
...@nmr.mgh.harvard.edu Cc: Veronica Popescu v.pope...@vumc.nl, Hugo Vrenken h.vren...@vumc.nl, freesurfer freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T2pial/FLAIRpial processing issues Hi Matt, Bruce, The problems are indeed a flirt issue, but given that it's programmed

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-15 Thread Martijn Steenwijk
, freesurfer freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T2pial/FLAIRpial processing issues Hi Matt, Bruce, The problems are indeed a flirt issue, but given that it's programmed with --init-fsl there is not much flexibility. However, from a FS point of view, it might

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-15 Thread Douglas N Greve
@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T2pial/FLAIRpial processing issues Hi Matt, Bruce, The problems are indeed a flirt issue, but given that it's programmed with --init-fsl there is not much flexibility

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-15 Thread Martijn Steenwijk
/FLAIRpial processing issues Hi Matt, Bruce, The problems are indeed a flirt issue, but given that it's programmed with --init-fsl there is not much flexibility. However, from a FS point of view, it might be a better

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-15 Thread Douglas N Greve
: [Freesurfer] T2pial/FLAIRpial processing issues Hi Matt, Bruce, The problems are indeed a flirt issue, but given that it's programmed with --init-fsl there is not much flexibility

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Matt Glasser
Popescu v.pope...@vumc.nl, Hugo Vrenken h.vren...@vumc.nl Subject: [Freesurfer] T2pial/FLAIRpial processing issues Dear all, There seem to be some serious issues with the T2pial / FLAIRpial processing options provided in the latest versions of FreeSurfer. First of all, although not clearly

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Bruce Fischl
Hi Martijn we can print warning and errors if FSLDIR is not set, but the registration errros seem to be mostly a flirt issue, no? Have you posted on the FSL list? Bruce On Thu, 14 Nov 2013, Martijn Steenwijk wrote: Dear all, There seem to be some serious issues with the T2pial /

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Martijn Steenwijk
Hi Matt, Bruce, The problems are indeed a flirt issue, but given that it's programmed with --init-fsl there is not much flexibility. However, from a FS point of view, it might be a better and more robust approach to first register FLAIRraw.mgz to raw.mgz, and then concatenate the resulting

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Matt Glasser
Steenwijk martijnsteenw...@gmail.com Date: Thursday, November 14, 2013 9:27 AM To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: Veronica Popescu v.pope...@vumc.nl, Hugo Vrenken h.vren...@vumc.nl, freesurfer freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T2pial/FLAIRpial processing issues Hi

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Bruce Fischl
AM To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: Veronica Popescu v.pope...@vumc.nl, Hugo Vrenken h.vren...@vumc.nl, freesurfer freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T2pial/FLAIRpial processing issues Hi Matt, Bruce,  The problems are indeed a flirt issue, but given that it's