Hello Everyone,

I have tried using both the original dicom files and the renamed brain voyager files and although it fixes the Talairach error for some subjects I keep getting the same error for others (I haven't noticed a pattern here). 

Error message:

#@# Talairach Failure Detection Mon Sep 15 11:03:51 PDT 2008
/Applications/freesurfer/subjects/2824mm/mri

\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)

Darwin guest-wireless-207-151-243-073.usc.edu 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386


Any idea what could be the cause?

many thanks,

Marissa

On Wed, Aug 20, 2008 at 9:08 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

yes, try the original dicoms. And post these to the list so others can answer!

On Wed, 20 Aug 2008, Marissa Gorlick wrote:

Hi Bruce,

Thank you for helping me join the mailing list.

My data is in DICOM format.  I did change the names of the files using a
brain voyager function before using freesurfer.  Could that have eliminated
the direction cosines from the files?

Thanks again,

Marissa

On Tue, Aug 19, 2008 at 7:35 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>wrote:

Can someone help Marissa get on the FreeSurfer mailing list? Marissa: what
format is your input data in? If it was analyze, then it probably does not
contain the information necessary to orient the images properly so that we
are failing to know which axis is front/back etc... You are *far* better off
using a format that retains the direction cosines (such as dicom or nifti).

cheers,
Bruce



On Tue, 19 Aug 2008, Marissa Gorlick wrote:

 Hello Freesurfer Owner,

I would like to post to your message board.  I attempted to join the
opensubscriber forum, however they never e-mailed me my activation code to
confirm my e-mail address.  I have registered freesurfer and received a
licence (through my e-mail address mgorlick@usc.edu).  Are there other
steps
I should take to become a part of the online freesurfer community?

Many thanks,

Marissa

---------- Forwarded message ----------
From: <freesurfer-owner@nmr.mgh.harvard.edu>
Date: Tue, Aug 19, 2008 at 4:38 PM
Subject: Talairach Failure Detection Help
To: cosmiccarrot@gmail.com


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---------- Forwarded message ----------
From: "Marissa Gorlick" <cosmiccarrot@gmail.com>
To: freesurfer@nmr.mgh.harvard.edu
Date: Tue, 19 Aug 2008 16:37:48 -0700
Subject: Talairach Failure Detection Help
Hello Freesurfer team,

My name is Marissa Gorlick and I am new to freesurfer.  I am trying to do
a
cortical thickness analysis but I am having trouble processing my data.

When I input the command:

recon-all -s <subjid> -all

The data processing begins for a few minutes and then spits out the error
message:

Tue Aug 19 16:18:54 PDT 2008
talairach_avi done
#--------------------------------------------
#@# Talairach Failure Detection Tue Aug 19 16:18:54 PDT 2008
/Applications/freesurfer/subjects/part_2/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
Darwin ger341-macbk2.usc.edu 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct
10
18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386

recon-all exited with ERRORS at Tue Aug 19 16:18:55 PDT 2008

I looked in the opensubscriber forum and saw a recommendation to use
the "Fixing
Bad Output From the Talairach Registration" tutorial to remedy the error.
Following the tutorial I ran:

tkregister2 --mgz --s <subjid> --fstal

The resulting output images look strange.  The TARGET image has low
contrast and can only be viewed in sagittal slices (which are, oddly,
displayed by clicking the coronal button).
The MOVEABLE view is stranger still displaying a very small squished
blurry image of the brain. (see attached images)

I would appreciate any advice you may have in how I should proceed
with the analysis.

Many thanks,

Marissa Gorlick

--
Marissa Gorlick
Mather Lab Manager
Phone: (213) 740 - 9543
Andrus Gerontology
3715 McClintock Ave.
Los Angeles, CA 90089-0191