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.
>
> 2. Making a 3T atlas representative target. I can make the
> target using your data.
> However, it is up to the FreeSurfer developers to decide how
> to proceed.
> Adding the control structures to enable use of input-dependent
> or user-selectable
> atlas representative target amounts to a revision.
> The FreeSurfer developers may or may not wish to undertake
> such
> a revision. In any case, it can't happen tomorrow.
>
> 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?
> >
> >2) As you mentioned, we can make a suitable 3T atlas-
> representative
> >target to resolve the Talairach transform problem. Now, we
> have several
> >dozens of adult Chinese 3T MPRAGE data. Would you please give
> us some cues
> >how to generate the 3T atlas target with FreeSurfer?
> >
>
> > Anyone has ideas on this issue,please let me know.
> >
> >Thanks again.
> >
> >Zonglei
> >
> >2009/4/20 Avi Snyder <a...@npg.wustl.edu>
>
> >
> >> Zonglei,
> >>
> >> The log files contain the string "t4_read:..... read error"
> >> This is a benign message indicating the the affine
> transform
> >> file was not found. This always occurs at the start of the
> >> affine transform sequence and carries no significance.
> >>
> >> Review of the log file indicates that in the case of
> subjA39
> >> Talairach atlas transform achieved a reasonable numeric
> result.
> >>
> >> In the case of subjA06 the Talairach transform did not
> achieve
> >> a good result. This is an algorithmic issue. It appears
> that
> >> the talairah_avi module was initiated twice, I assume, in
> an attmept
> >> to improve the result, but the result did not improve. In
> this
> >> log file the "read error" message occurs twice but it
> simply
> >> means that the transform sequence was initiated twice.
> >>
> >> So, there is a problem but the the "read error" message has
> nothing
> >> to do with it. Poor MP-RAGE to atlas representative target
> results
> >> most likely are attributable to use of a 1.5T target with
> 3T input.
> >> It this is correct, then a permanent solution to the
> problem could
> >> be achieved by selecting the
> >> atlas-representative target according to the MP-RAGE
> source.
> >> Generation of a suitable 3T target would not be difficult.
> >>
> >> Avi
> >> ------------------------------------------------------
> >> Date: Sun, 19 Apr 2009 22:52:35 +0800
> >> Subject: Re: [Freesurfer] t4_read error (fwd)
> >> From: Zhen Zonglei <zonglei....@gmail.com>
> >> To: Avi Snyder <a...@npg.wustl.edu>
> >> Cc: fis...@nmr.mgh.harvard.edu, ni...@nmr.mgh.harvard.edu,
> >> freesurfer@nmr.mgh.harvard.edu
> >>
> >> Hi avi:
> >>
> >> Thanks for your response, attachments are my recon-
> all.logs.
> >> If you have any ideas,please let me know.
> >>
> >> Thanks again.
> >>
> >> 2009/4/17 Avi Snyder <a...@npg.wustl.edu>
> >> -----------------------------------------------
> >> > Zonglei,
> >> >
> >> > Send the log file to
> >> >
> >> > a...@npg.wustl.edu
> >> > ----------------------------------------
> >> > >Date: Fri, 17 Apr 2009 11:15:19 -0400 (EDT)
> >> > >From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> >> > >To: Avi Snyder <a...@npg.wustl.edu>
> >> > >cc: ni...@nmr.mgh.harvard.edu
> >> > >
> >> > >do you want to contact him directly?
> >> > >
> >> > >On Fri, 17 Apr 2009, Avi Snyder wrote:
> >> > >
> >> > >> Most likely the MPRAGE->atlas computation aborted
> without creating
> >> > >> the relevant t4 file (ASCII representation of the
> affine transform).
> >> > >> This could occur if the images were somehow corrupted.
> >> > >>
> >> > >> Alternatively, the t4 file is present but a recent OS
> upgrade has
> >> caused
> >> > >> the previously compiled t4_read FORTRAN function to
> bomb. I have seen
> >> this
> >> case
> >> > >> once before and have therefore created an all-C t4 i/o
> module.
> >> > >>
> >> > >> We can distinguish these cases by asking if you got a
> core dump, of if
> >> > >> a t4 file is still present. The complete tal transform
> log file would
> >> > >> be diagnostically very helpful.
> >> > >>
> >> > >> Avi
> >> > >> ------------------------------------------
> >> > >>> Date: Fri, 17 Apr 2009 07:58:36 -0400 (EDT)
> >> > >>> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> >> > >>> To: Avi Snyder <a...@npg.wustl.edu>
> >> > >>> cc: Nick Schmansky <ni...@nmr.mgh.harvard.edu>
> >> > >>> Subject: [Freesurfer] t4_read error (fwd)
> >> > >>>
> >> > >>> Hi Avi,
> >> > >>>
> >> > >>> do you know what this message means?
> >> > >>>
> >> > >>> thanks
> >> > >>> Bruce
> >> > >>> ---------- Forwarded message ----------
> >> > >>> Date: Fri, 17 Apr 2009 19:32:05 +0800
> >> > >>> From: Zhen Zonglei <zonglei....@gmail.com>
> >> > >>> To: freesurfer@nmr.mgh.harvard.edu
> >> > >>> Subject: [Freesurfer] t4_read error
> >> > >>>
> >> > >>> Dear all:
> >> > >>> Recon-all has finished without error in my
> reconstruction. However,
> >> when I
> >> > >>> checked recon-all.log, I found three was a error
> “t4_read:
> >> > >>> talsrcimg_to_711-2C_as_mni_average_305_t4 read
> error”.
> >> > >>>
> >> > >>> What's this error mean? Does it have some effects on
> my
> >> reconstruction?
> >> > >>>
> >> > >>> Thanks
> >> > >>>
> >> > >>> --
> >> > >>> Zonglei Zhen, PhD
> >> > >>> Assistant Professor of Cognitive Neuroscience
> >> > >>> BNU Imaging Center for Brain Research, State Key
> Laboratory of
> >> > Cognitive
> >> > >>> Neuroscience and Learning, P.R. China
> >> --
> >> Zonglei Zhen, PhD
> >> Assistant Professor of Cognitive Neuroscience
> >> BNU Imaging Center for Brain Research, State Key Laboratory
> of Cognitive
> >> Neuroscience and Learning, P.R. China
> >
> >--
> >Zonglei Zhen, PhD
> >Assistant Professor of Cognitive Neuroscience
> >BNU Imaging Center for Brain Research, State Key Laboratory
> of Cognitive
> >Neuroscience and Learning, P.R. China
>
>
> BEGIN {go = 0;}
>
> (NF == 6 && go > 0) {
> for (i = 1; i <= 6; i++) p[k++] = $i;
> go++; if (go == 3) {go = 0;}
> }
>
> /eta,q/ {p[k++] = $2;}
>
> /second partial in parameter space/ {go++; k = 0;}
>
> END {
> for (k = 0; k < 12; k++) printf ("%5.0f", p[k]);
> printf ("%10.5f\n", p[12]);
> }
>
>
>
>
>
> --
> Zonglei Zhen, PhD
> Assistant Professor of Cognitive Neuroscience
> BNU Imaging Center for Brain Research, State Key Laboratory of
> Cognitive Neuroscience and Learning, P.R. China
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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