Nick,
Could you please help me reconcile your reply to Zhen below with Avis
note below about the tal_QC_AZS script?
Below we have pasted a sample of our recon all log. Is the talAviQA in
the default log the same as the eta term that Avi describes as output of
the tal_QC_AZS script below in his note to Zhen? What does the z refer to
in the recon all log?
It appears that the default tal check does not generate the
atlas_transform_error term, correct? ( I also dont see any term less
than 15).
Does one need to run Avis tal_QC_AZS script to generate the
atlas_transform_error term ?
While it looks like tal check not not automatically output the value of
the atlas_transform_error term,
Is the z score that DOES appear (automatically) in the log file the same z
score that Avi mentions below, that compares the atlas_transform_error
term to the training set?
Thanks!
Carl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
------------------------------------------------------------------------------------------------------------------------------
Mon Apr 13 15:14:55 CST 2009
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#...@# Talairach Failure Detection Mon Apr 13 15:14:56 CST 2009
/nfs/h2/r6/subjects/A39/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8116,
pval=0.8469 >= threshold=0.0050)
awk -f
/nfs/h1/r1/jliu/new_soft_test/freesurfer/bin/extract_talairach_avi_QA.awk
/nfs/h2/r6/subjects/A39/mri/transforms/talairach_avi.log
TalAviQA: 0.97187
z-score: -1
#-------------------------------------------
On 4/22/09 4:04 PM, "Nick Schmansky" <ni...@nmr.mgh.harvard.edu> wrote:
Zhen,
The -tal-check flag included with recon-all will perform the QA check
that Avi mentions, with the addition of creating a z-score comparing the
subject's QA score to a set of QA scores of known-good talairach
alignments. The -tal-check flag runs by default in recon-all (in -all
and -autorecon1), and will error exit if the alignment is below
threshold.
Nick
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
On Tue, 2009-04-21 at 19:02 +0800, Zhen Zonglei wrote:
> Dear Avi:
>
> Thanks for your kind and the script.I will use it to check tal QC of
> all my data .
>
> Zognlei
>
>
> 2009/4/21 Avi Snyder <a...@npg.wustl.edu>
> Zonglei,
>
> 1. Re: how to detemine Talairach transform success from the
> logfile:
> Attached is a simple csh script (tal_QC_AZS) and a required
> awk script.
> tal_QC_AZS reads the log file and writes out two numbers.
> The first number (eta) is the spatial correlation between the
> (blurred) input
> image and the atlas representative target image. eta values
> less than 0.96 are highly
> suspect. The second number ("atlas_transform_error") is
> computed on the basis of
> registration objective function curvature in parameter space.
> The 12 present numbers
> are compared to values derived from a training set.
> atlas_transform_error values
> less than ~15 are good.
>
>
> Avi
>
> -----------------------------------------------------------------------
> >Date: Tue, 21 Apr 2009 12:52:45 +0800
> >Subject: Re: [Freesurfer] t4_read error (fwd)
> >From: Zhen Zonglei <zonglei....@gmail.com>
> >To: Avi Snyder <a...@npg.wustl.edu>
>
> >Cc: freesurfer@nmr.mgh.harvard.edu,
> fis...@nmr.mgh.harvard.edu, ni...@nmr.mgh.harvard.edu
> >
> > Hi avi:
> >
> >Thanks for your help. Still have two questions.
> >
> >1) How to determine whether the Talairach transform is
> reasonable
> >based on recon-all.log?
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
