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 avi@npg.wustl.edu
Zonglei,
- 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.
- 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.fsl@gmail.com To: Avi Snyder avi@npg.wustl.edu Cc: freesurfer@nmr.mgh.harvard.edu, fischl@nmr.mgh.harvard.edu,
nicks@nmr.mgh.harvard.edu
Hi avi:
Thanks for your help. Still have two questions.
How to determine whether the Talairach transform is reasonablebased on recon-all.log?
As you mentioned, we can make a suitable 3T atlas-representativetarget 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 avi@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.fsl@gmail.com To: Avi Snyder avi@npg.wustl.edu Cc: fischl@nmr.mgh.harvard.edu, nicks@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 avi@npg.wustl.edu
Zonglei,
Send the log file to
avi@npg.wustl.edu
Date: Fri, 17 Apr 2009 11:15:19 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Avi Snyder avi@npg.wustl.edu cc: nicks@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 fischl@nmr.mgh.harvard.edu > To: Avi Snyder avi@npg.wustl.edu > cc: Nick Schmansky nicks@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.fsl@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]); }
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 avi@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.fsl@gmail.com> >To: Avi Snyder <avi@npg.wustl.edu> >Cc: freesurfer@nmr.mgh.harvard.edu, fischl@nmr.mgh.harvard.edu, nicks@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 <avi@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.fsl@gmail.com> >> To: Avi Snyder <avi@npg.wustl.edu> >> Cc: fischl@nmr.mgh.harvard.edu, nicks@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 <avi@npg.wustl.edu> >> ----------------------------------------------- >> > Zonglei, >> > >> > Send the log file to >> > >> > avi@npg.wustl.edu >> > ---------------------------------------- >> > >Date: Fri, 17 Apr 2009 11:15:19 -0400 (EDT) >> > >From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> >> > >To: Avi Snyder <avi@npg.wustl.edu> >> > >cc: nicks@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 <fischl@nmr.mgh.harvard.edu> >> > >>> To: Avi Snyder <avi@npg.wustl.edu> >> > >>> cc: Nick Schmansky <nicks@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.fsl@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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi NIck: Thanks for your information. I always use recon-all with -all option to reconstruct my data, and the command can successfully finished, Does it mean that I have got a good tal transform? subjA06 also has been reconstructed with recon-all, but it did not get a good tal transform as Avi checked. Why not tal-check flag report error ? Its criterion is different from Avi?
Thanks again.
Zonglei 2009/4/23 Nick Schmansky nicks@nmr.mgh.harvard.edu
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 avi@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.fsl@gmail.com> >To: Avi Snyder <avi@npg.wustl.edu> >Cc: freesurfer@nmr.mgh.harvard.edu, fischl@nmr.mgh.harvard.edu, nicks@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 <avi@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.fsl@gmail.com> >> To: Avi Snyder <avi@npg.wustl.edu> >> Cc: fischl@nmr.mgh.harvard.edu, nicks@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 <avi@npg.wustl.edu> >> ----------------------------------------------- >> > Zonglei, >> > >> > Send the log file to >> > >> > avi@npg.wustl.edu >> > ---------------------------------------- >> > >Date: Fri, 17 Apr 2009 11:15:19 -0400 (EDT) >> > >From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> >> > >To: Avi Snyder <avi@npg.wustl.edu> >> > >cc: nicks@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 <fischl@nmr.mgh.harvard.edu> >> > >>> To: Avi Snyder <avi@npg.wustl.edu> >> > >>> cc: Nick Schmansky <nicks@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.fsl@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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Nick Schmansky -
Zhen Zonglei