yes, definitely. The dicoms are best
On Tue, 27 Aug 2013, pablo najt wrote:
Thank you very much for your input. Yes, I did start with analyze format and
also I have visually inspected the images. Almost all my
scans consistently show an extended whole in the prefrontal area (with a few
exception of some scans showing this in posterior
locations).
I am assuming the best is to start with either DICOM or NIFTI and avoid analyze
format. Is this correct?
Best,
Pablo
Date: Tue, 27 Aug 2013 12:08:22 -0400
From: fis...@nmr.mgh.harvard.edu
To: pablon...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed
incorrect? What input format did you start with? Most of these occur
because people start with analyze, which doesn't have the direction
cosines, and so the data is oriented incorrectly
cheers
Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
> Dear FS experts,I am contacting you to report an error after launching recon
-all for one of my subjects (see below). I am using a
> macbook pro with snow leopard version 10.6.8.
>
> I would greatly appreciate if you could advise me which step/s should I take to correct this.
> Thank you for your attention,
> Pablo
>
> Error:-------------------------------------------------------------------------------------------------------------------------------
-
> ------------------
> #@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013
> /Users/pablonajt/subjects/tr5713/mri
> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***
(p=0.0554, pval=0.0034 < threshold=0.0050)
> Manual Talairach alignment may be necessary, or
> include the -notal-check flag to skip this test,
> making sure the -notal-check flag follows -all
> or -autorecon1 in the command string.
> See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
> Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue
Jun 7 16:33:36 PDT 2011;
> root:xnu-1504.15.3~1/RELEASE_I386 i386
>
> recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
>
>
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