subject:"\[Freesurfer\] MCSRCH error"

Re: [Freesurfer] MCSRCH error using sample data (001.mgz and 002.mgz)

2021-04-09 Thread Fischl, Bruce

Hi Yoonho

That warning is usually benign. Does the recon finish ok?
Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Yoonho Hwang
Sent: Friday, April 9, 2021 2:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] MCSRCH error using sample data (001.mgz and 002.mgz)

External Email - Use Caution
Hello FreeSurfer Developers,

I'm attempting to compute cortical thickness and to analyze it between groups.
So I perform "recon-all", but rather than using recon-all -all, some problems 
arise while performing each of the steps in it. These problems are as follwing.

sample-001.mgz and sample-002.mgz in /usr/local/freesurfer/subjects/ are used. 
What is this problem happening?
IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN 
OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR 
INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.10
Resulting transform:
 1.09487  -0.03668   0.00057  -10.07315;
 0.03682   1.10413   0.22705  -54.96997;
-0.00899  -0.18307   0.95770   22.82867;
 0.0   0.0   0.0   1.0;

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
2) Platform: Ubuntu release 18.04.1
3) uname -a: Linux LABPC 5.4.0-70-generic #78~18.04.1-Ubuntu SMP Sat Mar 20 
14:10:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached

Thank you very much.

Sincerely,
Yoonho

--
Hwang, Yoonho

Medical Image Processing Laboratory (MIPL),
Department of Biomedical Engineering, Yonsei University.

#218 Sanhak-Kwan, 1, Yeonsedae-gil, Heungeop-myeon, Wonju,
Gangwon-do, 26493, Republic of Korea.

Office: +82-33-760-2499
Email: ken.lmsta...@gmail.com<mailto:ken.lmsta...@gmail.com>
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[Freesurfer] MCSRCH error using sample data (001.mgz and 002.mgz)

2021-04-08 Thread Yoonho Hwang

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compute cortical thickness and to analyze it between
groups.
So I perform "recon-all", but rather than using recon-all -all, some
problems arise while performing each of the steps in it. These problems are
as follwing.

*sample-001.mgz and sample-002.mgz in /usr/local/freesurfer/**subjects/ are
used. What is this problem happening? *

*IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) =
-0.0  tol 0.10*
*Resulting transform:*
* 1.09487  -0.03668   0.00057  -10.07315;*
* 0.03682   1.10413   0.22705  -54.96997;*
*-0.00899  -0.18307   0.95770   22.82867;*
* 0.0   0.0   0.0   1.0;*


1) FreeSurfer version:
freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
2) Platform: Ubuntu release 18.04.1
3) uname -a: Linux LABPC 5.4.0-70-generic #78~18.04.1-Ubuntu SMP Sat Mar 20
14:10:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached

Thank you very much.

Sincerely,
Yoonho


-- 
*Hwang, Yoonho*
*Medical Image Processing Laboratory (MIPL),*
*Department of Biomedical Engineering, Yonsei University.*

*#218 Sanhak-Kwan, 1, Yeonsedae-gil, Heungeop-myeon, Wonju,*
*Gangwon-do, 26493, Republic of Korea.*

*Office: +82-33-760-2499*
*Email: ken.lmsta...@gmail.com *
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Re: [Freesurfer] MCSRCH ERROR

2013-08-14 Thread Bruce Fischl


yes, probably
On Wed, 14 Aug 2013, Eli Fredman wrote:


Thanks for the quick response Bruce. Is that missing patch the reason that
it did not create a wmparc.mgz file in any of our cases?


On Wed, Aug 14, 2013 at 10:47 AM, Bruce Fischl 
wrote:
  Hi Eli

  I don't think that's an error, just an arcane warning that some
  open source numerical minimization code complains about
  sometimes. Looking at the log it seems like it completed ok,
  although this is the version of 5.3 without the segstats/ribbon
  patch, which you will probably want to download (can someone
  point Eli at this?)

  cheers
  Bruce




  On Wed, 14 Aug 2013, Eli Fredman wrote:

I ran 10 cases through freesurfer5.3 last night and
found that they all
exited with the same error. This is the input that I
used:


recon-all-i/projects/schiz/NFL/case01409/strct/align-space/01409-t1w-realign-masked.
ni
i.gz -autorecon1 -noskullstrip -subjid 01409 && cp
subjects/01409/mri/T1.mgz
subjects/01409/mri/brainmask.mgz && recon-all
-autorecon2 -subjid 01409 &&
recon-all -autorecon3 -subjid 01409

I've attached the recon-all.log file which shows the
following error:

 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF
ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES:
FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof
QuasiNewtonEMA: 007: -log(p) =  
-0.0  tol 0.10

(as a side note, the reason I don't simply run
recon-all -all is because
this doesn't seem to acknowledge the -noskullstrip
tag).


Thanks for the help!

--
Eli Fredman, BA
Research Assistant
Psychiatry Neuroimaging Laboratory
Harvard Medical School, Brigham and Women's Hospital
1249 Boylston St, 3rd Floor
Boston, MA 02215
Office: (617) 525-6118
Cell: (314) 952-8098
Fax: (617) 525-6150




--
Eli Fredman, BA
Research Assistant
Psychiatry Neuroimaging Laboratory
Harvard Medical School, Brigham and Women's Hospital
1249 Boylston St, 3rd Floor
Boston, MA 02215
Office: (617) 525-6118
Cell: (314) 952-8098
Fax: (617) 525-6150

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Re: [Freesurfer] MCSRCH ERROR

2013-08-14 Thread Eli Fredman

Thanks for the quick response Bruce. Is that missing patch the reason that
it did not create a wmparc.mgz file in any of our cases?


On Wed, Aug 14, 2013 at 10:47 AM, Bruce Fischl
wrote:

> Hi Eli
>
> I don't think that's an error, just an arcane warning that some open
> source numerical minimization code complains about sometimes. Looking at
> the log it seems like it completed ok, although this is the version of 5.3
> without the segstats/ribbon patch, which you will probably want to download
> (can someone point Eli at this?)
>
> cheers
> Bruce
>
>
>
>
>
> On Wed, 14 Aug 2013, Eli Fredman wrote:
>
>  I ran 10 cases through freesurfer5.3 last night and found that they all
>> exited with the same error. This is the input that I used:
>>
>> recon-all -i/projects/schiz/NFL/**case01409/strct/align-space/01**
>> 409-t1w-realign-masked.ni 
>> i.gz -autorecon1 -noskullstrip -subjid 01409 && cp
>> subjects/01409/mri/T1.mgz
>> subjects/01409/mri/brainmask.**mgz && recon-all -autorecon2 -subjid
>> 01409 &&
>> recon-all -autorecon3 -subjid 01409
>>
>> I've attached the recon-all.log file which shows the following error:
>>
>>  IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
>> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
>> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) =
>> -0.0  tol 0.10
>>
>> (as a side note, the reason I don't simply run recon-all -all is because
>> this doesn't seem to acknowledge the -noskullstrip tag).
>>
>>
>> Thanks for the help!
>>
>> --
>> Eli Fredman, BA
>> Research Assistant
>> Psychiatry Neuroimaging Laboratory
>> Harvard Medical School, Brigham and Women's Hospital
>> 1249 Boylston St, 3rd Floor
>> Boston, MA 02215
>> Office: (617) 525-6118
>> Cell: (314) 952-8098
>> Fax: (617) 525-6150
>>
>>


-- 
Eli Fredman, BA
Research Assistant
Psychiatry Neuroimaging Laboratory
Harvard Medical School, Brigham and Women's Hospital
1249 Boylston St, 3rd Floor
Boston, MA 02215
Office: (617) 525-6118
Cell: (314) 952-8098
Fax: (617) 525-6150
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] MCSRCH ERROR

2013-08-14 Thread Bruce Fischl


Hi Eli

I don't think that's an error, just an arcane warning that some open 
source numerical minimization code complains about sometimes. Looking at 
the log it seems like it completed ok, although this is the version of 5.3 
without the segstats/ribbon patch, which you will probably want to download 
(can someone point Eli at this?)


cheers
Bruce




On Wed, 14 Aug 2013, Eli Fredman wrote:


I ran 10 cases through freesurfer5.3 last night and found that they all
exited with the same error. This is the input that I used:

recon-all 
-i/projects/schiz/NFL/case01409/strct/align-space/01409-t1w-realign-masked.ni
i.gz -autorecon1 -noskullstrip -subjid 01409 && cp subjects/01409/mri/T1.mgz
subjects/01409/mri/brainmask.mgz && recon-all -autorecon2 -subjid 01409 &&
recon-all -autorecon3 -subjid 01409

I've attached the recon-all.log file which shows the following error:

 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) =  
-0.0  tol 0.10

(as a side note, the reason I don't simply run recon-all -all is because
this doesn't seem to acknowledge the -noskullstrip tag).


Thanks for the help!

--
Eli Fredman, BA
Research Assistant
Psychiatry Neuroimaging Laboratory
Harvard Medical School, Brigham and Women's Hospital
1249 Boylston St, 3rd Floor
Boston, MA 02215
Office: (617) 525-6118
Cell: (314) 952-8098
Fax: (617) 525-6150

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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] MCSRCH ERROR

2012-06-06 Thread Bruce Fischl

I think the linesearch message is a red herring. We've seen it lots of 
times when the process runs fine. Are you sure some that there isn't 
something else?

On Wed, 6 Jun 2012, Jeff Thompson wrote:

> Hi -
> 
> Was there ever a solution found for this? I am currently having the same 
> problem.
> 
> Thanks,
> 
> Jeff Thompson
> 
> Can you send us e recon-all.log file?
> 
> 
> 
> On Aug 8, 2011, at 4:30 AM, "Irwin, William"  
> wrote:
> 
> > Hi-
> > 
> > 
> > 
> > I?m at a bit of a loss as to how to address and/or fix these errors.
> > 
> > 
> > 
> > The native input images are very good quality; the conversion to T1.mgz is 
> > fine; the brainmask.mgz is good,
>  a bit of dura remained at the parietal/occipital region (very common); 
> otherwise, the skull stripping is ver
> y clean.
> > 
> > 
> > 
> > The recon-all ?finished? but with errors as expected. Processing 
> > ?continued? to the end, but there is no output exc
> ept in /mri and /touch.
> > 
> > 
> > 
> > Doing: #@# Skull Stripping
> > 
> > 
> > 
> > First under ?Computing MAP estimate using 3481 samples...?
> > 
> > 
> > 
> > IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> > RETURN OF LINE SEARCH: INFO= 3 POS
> SIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof 
> QuasiNewtonEMA: 005: -log(p) = 
> 10327.2  tol 0.10
> > 
> > 
> > 
> > Then several of the same under ?EM alignment process ...?
> > 
> > 
> > 
> > IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> > RETURN OF LINE SEARCH: INFO= 3 POS
> SIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 
> 2 through quasi-newton minimizat
> ion...
> > 
> > 
> > 
> > IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> > RETURN OF LINE SEARCH: INFO= 3 POS
> SIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 
> 3 through quasi-newton minimizat
> ion...
> > 
> > 
> > 
> > IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> > RETURN OF LINE SEARCH: INFO= 3 POS
> SIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 
> 4 through quasi-newton minimizat
> ion...
> > 
> > 
> > 
> > IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> > RETURN OF LINE SEARCH: INFO= 3 POS
> SIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 
> 5 through quasi-newton minimizat
> ion...
> > 
> > 
> > 
> > IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> > RETURN OF LINE SEARCH: INFO= 3 POS
> SIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof 
> QuasiNewtonEMA: 017: -log(p) = 
> 1145822.4  tol 0.00
> > 
> > 
> > 
> > Then again at ?Computing MAP estimate using 2772 samples...?
> > 
> > 
> > 
> > IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> > RETURN OF LINE SEARCH: INFO= 3 POS
> SIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof 
> QuasiNewtonEMA: 009: -log(p) = 
> 7006.0  tol 0.10
> > 
> > 
> > 
> > IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> > RETURN OF LINE SEARCH: INFO= 3 POS
> SIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 
> 2 through quasi-newton minimizat
> ion...
> > 
> > 
> > 
> > IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> > RETURN OF LINE SEARCH: INFO= 3 POS
> SIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof 
> QuasiNewtonEMA: 013: -log(p) = 
> 838978.4  tol 0.00
> > 
> > 
> > 
> > Thanks,
> > 
> > Wil
> > 
> > 
> > 
> > 
> > William Irwin | Brain Imaging Coordinator
> > UCSF | Memory and Aging Center
> > 350 Parnassus Avenue, Suite 905
> > San Francisco  CA  94143-1207
> > wirwin at memory.ucsf.edu | memory.ucsf.edu
> > p: 415.476.1680 | f: 415.476.1816
> > 
> > 
> 
> 
>
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Re: [Freesurfer] MCSRCH ERROR

2012-06-06 Thread Jeff Thompson


Hi -

Was there ever a solution found for this? I am currently having the same 
problem.

Thanks,

Jeff Thompson

Can you send us e recon-all.log file?



On Aug 8, 2011, at 4:30 AM, "Irwin, William"  wrote:

> Hi-
> 
>  
> 
> I’m at a bit of a loss as to how to address and/or fix these errors.
> 
>  
> 
> The native input images are very good quality; the conversion to T1.mgz is 
> fine; the brainmask.mgz is good, a bit of dura remained at the 
> parietal/occipital region (very common); otherwise, the skull stripping is 
> very clean.
> 
>  
> 
> The recon-all “finished” but with errors as expected. Processing “continued” 
> to the end, but there is no output except in /mri and /touch.
> 
>  
> 
> Doing: #@# Skull Stripping
> 
>  
> 
> First under “Computing MAP estimate using 3481 samples...”
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10327.2 
>  tol 0.10
> 
>  
> 
> Then several of the same under “EM alignment process ...”
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization...
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESpass 4 through quasi-newton minimization...
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESpass 5 through quasi-newton minimization...
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 017: -log(p) = 
> 1145822.4  tol 0.00
> 
>  
> 
> Then again at “Computing MAP estimate using 2772 samples...”
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 7006.0  
> tol 0.10
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 
> 838978.4  tol 0.00
> 
>  
> 
> Thanks,
> 
> Wil
> 
>  
> 
> 
> William Irwin | Brain Imaging Coordinator
> UCSF | Memory and Aging Center
> 350 Parnassus Avenue, Suite 905
> San Francisco  CA  94143-1207
> wirwin at memory.ucsf.edu | memory.ucsf.edu
> p: 415.476.1680 | f: 415.476.1816
> 
>  
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Re: [Freesurfer] MCSRCH ERROR

2011-10-20 Thread Bruce Fischl

I just took a look at it, and I think it's still running. How long has it 
been? There looks like there is a very large topological defect, that will 
take a long time to correct. The correction has complexity that is 
quadratic in the convex hull of the largest defect, so large ones can take 
a *long* time. Usually when there is one this big though it means something 
failed. Check the rh.inflated.nofix and rh.orig.nofix files to see if there 
is a connection to the skull or something else. If you have trouble fixing 
this, upload the subject and we'll take a look.

cheers
Bruce

On Thu, 20 Oct 2011, Kenichiro Tanaka wrote:

> Dear Bruce,
>
> I emailed you the recon-all.log.
> Please check it and tell me how wrong something is?
>
> Thanks,
>
> Kenichiro Tanaka.
>
> (2011/10/19 21:26), Bruce Fischl wrote:
>>  ok, why don't you tar and gzip the subject and put it on our ftp site. You
>>  can also just email me the recon-all.log and I'll take a look
>>  Bruce
>>  On Wed, 19 Oct 2011, Kenichiro Tanaka wrote:
>> 
>> >  Dear Bruce,
>> > 
>> >  I think they are error.
>> >  The number of output files is not complete.
>> >  For example, there are only lh.aparc.a2009s.stats, lh.aparc.stats and
>> >  lh.curv.stats on stats directory.
>> > 
>> >  Thanks,
>> > 
>> >  Kenichiro Tanaka.
>> > 
>> > 
>> > 
>> >  (2011/10/18 21:30), Bruce Fischl wrote:
>> >Are you sure they are errors? We see this mysterious message
>> >sometimes, but I don't think it is really an error, and usually
>> >things are fine
>> > 
>> >cheers
>> >Bruce
>> > 
>> >On Tue, 18 Oct 2011, Kenichiro Tanaka wrote:
>> > 
>> >  Hello All,
>> > 
>> >  While processing a brain image data(.mgz) through
>> >  ver5.0.0, I got the
>> >  following errors.
>> >  I have no idea how to resolve them.
>> >  I need outputs in stats directory, there are only
>> >  lh.aparc.a2009s.stats,
>> >  lh.aparc.stats, and lh.curv.stats.
>> >  What caused them?
>> >  How should I resolve them?
>> > 
>> >  IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF
>> >  ROUTINE MCSRCH ERROR
>> >  RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES:
>> >  FUNCTION OR GRADIENT ARE
>> >  INCORRECT OR INCORRECT TOLERANCESoutof
>> >  QuasiNewtonEMA: 005: -log(p) =
>> >  10318.1 tol 0.10
>> >  .
>> >  .
>> >  .
>> >  inflating to sphere (rms error < 2.00)
>> >  000: dt: 0., rms radial error=175.699, avgs=0
>> >  005/300: dt: 0.9000, rms radial error=175.446,
>> >  avgs=0
>> >  010/300: dt: 0.9000, rms radial error=174.904,
>> >  avgs=0
>> >  015/300: dt: 0.9000, rms radial error=174.193,
>> >  avgs=0
>> >  020/300: dt: 0.9000, rms radial error=173.383,
>> >  avgs=0
>> >  025/300: dt: 0.9000, rms radial error=172.518,
>> >  avgs=0
>> >  030/300: dt: 0.9000, rms radial error=171.620,
>> >  avgs=0
>> >  035/300: dt: 0.9000, rms radial error=170.706,
>> >  avgs=0
>> >  040/300: dt: 0.9000, rms radial error=169.784,
>> >  avgs=0
>> >  045/300: dt: 0.9000, rms radial error=168.860,
>> >  avgs=0
>> >  050/300: dt: 0.9000, rms radial error=167.935,
>> >  avgs=0
>> >  055/300: dt: 0.9000, rms radial error=167.012,
>> >  avgs=0
>> >  060/300: dt: 0.9000, rms radial error=166.092,
>> >  avgs=0
>> >  065/300: dt: 0.9000, rms radial error=165.175,
>> >  avgs=0
>> >  070/300: dt: 0.9000, rms radial error=164.262,
>> >  avgs=0
>> >  075/300: dt: 0.9000, rms radial error=163.352,
>> >  avgs=0
>> >  080/300: dt: 0.9000, rms radial error=162.447,
>> >  avgs=0
>> >  085/300: dt: 0.9000, rms radial error=161.547,
>> >  avgs=0
>> >  090/300: dt: 0.9000, rms radial error=160.651,
>> >  avgs=0
>> >  095/300: dt: 0.9000, rms radial error=159.759,
>> >  avgs=0
>> >  100/300: dt: 0.9000, rms radial error=158.871,
>> >  avgs=0
>> >  105/300: dt: 0.9000, rms radial error=157.989,
>> >  avgs=0
>> >  110/300: dt: 0.9000, rms radial error=157.110,
>> >  avgs=0
>> >  115/300: dt: 0.9000, rms radial error=156.236,
>> >  avgs=0
>> >  120/300: dt: 0.9000, rms radial error=155.367,
>> >  avgs=0
>> >  125/300: dt: 0.9000, rms radial error=154.502,
>> >  avgs=0
>> >  130/300: dt: 0.9000, rms radial error=153.642,
>> >

Re: [Freesurfer] MCSRCH ERROR

2011-10-18 Thread Bruce Fischl

Are you sure they are errors? We see this mysterious message sometimes, 
but I don't think it is really an error, and usually things are fine

cheers
Bruce

On Tue, 18 Oct 2011, Kenichiro Tanaka wrote:

> Hello All,
>
> While processing a brain image data(.mgz) through ver5.0.0, I got the
> following errors.
> I have no idea how to resolve them.
> I need outputs in stats directory, there are only lh.aparc.a2009s.stats,
> lh.aparc.stats, and lh.curv.stats.
> What caused them?
> How should I resolve them?
>
> IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) =
> 10318.1 tol 0.10
> .
> .
> .
> inflating to sphere (rms error < 2.00)
> 000: dt: 0., rms radial error=175.699, avgs=0
> 005/300: dt: 0.9000, rms radial error=175.446, avgs=0
> 010/300: dt: 0.9000, rms radial error=174.904, avgs=0
> 015/300: dt: 0.9000, rms radial error=174.193, avgs=0
> 020/300: dt: 0.9000, rms radial error=173.383, avgs=0
> 025/300: dt: 0.9000, rms radial error=172.518, avgs=0
> 030/300: dt: 0.9000, rms radial error=171.620, avgs=0
> 035/300: dt: 0.9000, rms radial error=170.706, avgs=0
> 040/300: dt: 0.9000, rms radial error=169.784, avgs=0
> 045/300: dt: 0.9000, rms radial error=168.860, avgs=0
> 050/300: dt: 0.9000, rms radial error=167.935, avgs=0
> 055/300: dt: 0.9000, rms radial error=167.012, avgs=0
> 060/300: dt: 0.9000, rms radial error=166.092, avgs=0
> 065/300: dt: 0.9000, rms radial error=165.175, avgs=0
> 070/300: dt: 0.9000, rms radial error=164.262, avgs=0
> 075/300: dt: 0.9000, rms radial error=163.352, avgs=0
> 080/300: dt: 0.9000, rms radial error=162.447, avgs=0
> 085/300: dt: 0.9000, rms radial error=161.547, avgs=0
> 090/300: dt: 0.9000, rms radial error=160.651, avgs=0
> 095/300: dt: 0.9000, rms radial error=159.759, avgs=0
> 100/300: dt: 0.9000, rms radial error=158.871, avgs=0
> 105/300: dt: 0.9000, rms radial error=157.989, avgs=0
> 110/300: dt: 0.9000, rms radial error=157.110, avgs=0
> 115/300: dt: 0.9000, rms radial error=156.236, avgs=0
> 120/300: dt: 0.9000, rms radial error=155.367, avgs=0
> 125/300: dt: 0.9000, rms radial error=154.502, avgs=0
> 130/300: dt: 0.9000, rms radial error=153.642, avgs=0
> 135/300: dt: 0.9000, rms radial error=152.786, avgs=0
> 140/300: dt: 0.9000, rms radial error=151.934, avgs=0
> 145/300: dt: 0.9000, rms radial error=151.087, avgs=0
> 150/300: dt: 0.9000, rms radial error=150.245, avgs=0
> 155/300: dt: 0.9000, rms radial error=149.407, avgs=0
> 160/300: dt: 0.9000, rms radial error=148.573, avgs=0
> 165/300: dt: 0.9000, rms radial error=147.744, avgs=0
> 170/300: dt: 0.9000, rms radial error=146.919, avgs=0
> 175/300: dt: 0.9000, rms radial error=146.098, avgs=0
> 180/300: dt: 0.9000, rms radial error=145.282, avgs=0
> 185/300: dt: 0.9000, rms radial error=144.470, avgs=0
> 190/300: dt: 0.9000, rms radial error=143.663, avgs=0
> 195/300: dt: 0.9000, rms radial error=142.860, avgs=0
> 200/300: dt: 0.9000, rms radial error=142.061, avgs=0
> 205/300: dt: 0.9000, rms radial error=141.266, avgs=0
> 210/300: dt: 0.9000, rms radial error=140.476, avgs=0
> 215/300: dt: 0.9000, rms radial error=139.693, avgs=0
> 220/300: dt: 0.9000, rms radial error=138.914, avgs=0
> 225/300: dt: 0.9000, rms radial error=138.140, avgs=0
> 230/300: dt: 0.9000, rms radial error=137.370, avgs=0
> 235/300: dt: 0.9000, rms radial error=136.604, avgs=0
> 240/300: dt: 0.9000, rms radial error=135.842, avgs=0
> 245/300: dt: 0.9000, rms radial error=135.085, avgs=0
> 250/300: dt: 0.9000, rms radial error=134.332, avgs=0
> 255/300: dt: 0.9000, rms radial error=133.583, avgs=0
> 260/300: dt: 0.9000, rms radial error=132.838, avgs=0
> 265/300: dt: 0.9000, rms radial error=132.098, avgs=0
> 270/300: dt: 0.9000, rms radial error=131.362, avgs=0
> 275/300: dt: 0.9000, rms radial error=130.629, avgs=0
> 280/300: dt: 0.9000, rms radial error=129.901, avgs=0
> 285/300: dt: 0.9000, rms radial error=129.177, avgs=0
> 290/300: dt: 0.9000, rms radial error=128.456, avgs=0
> 295/300: dt: 0.9000, rms radial error=127.740, avgs=0
> 300/300: dt: 0.9000, rms radial error=127.028, avgs=0
>
> spherical inflation complete.
> .
> .
> .
> epoch 4 (K=1280.0), pass 1, starting sse = 541.21
> taking momentum steps...
> taking momentum steps...
> taking momentum steps...
> pass 1 complete, delta sse/iter = 0.32/19 = 0.01710
> finalwriting spherical brain to ../surf/lh.qsphere.nofix
> spherical transformation took 0.10 hours
> distance error %10.00
> .
> .
> .
> pass 1: epoch 1 of 3 starting distance error %21.36
> pass 1: epoch 2 of 3 starting distance error %21.04
> unfolding complete - removing small folds...
> starting distance error %20.80
> removing remaining folds...
> final distance error %20.81
> 364: 0 negative triangles
> .
> .
> .
>
>
> Thanks,
>
> Kenichiro Tanaka.
>
> ___
> Freesurfer mailing list
>

[Freesurfer] MCSRCH ERROR

2011-10-18 Thread Kenichiro Tanaka

Hello All,

While processing a brain image data(.mgz) through ver5.0.0, I got the
following errors.
I have no idea how to resolve them.
I need outputs in stats directory, there are only lh.aparc.a2009s.stats,
lh.aparc.stats, and lh.curv.stats.
What caused them?
How should I resolve them?

IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) =
10318.1 tol 0.10
.
.
.
inflating to sphere (rms error < 2.00)
000: dt: 0., rms radial error=175.699, avgs=0
005/300: dt: 0.9000, rms radial error=175.446, avgs=0
010/300: dt: 0.9000, rms radial error=174.904, avgs=0
015/300: dt: 0.9000, rms radial error=174.193, avgs=0
020/300: dt: 0.9000, rms radial error=173.383, avgs=0
025/300: dt: 0.9000, rms radial error=172.518, avgs=0
030/300: dt: 0.9000, rms radial error=171.620, avgs=0
035/300: dt: 0.9000, rms radial error=170.706, avgs=0
040/300: dt: 0.9000, rms radial error=169.784, avgs=0
045/300: dt: 0.9000, rms radial error=168.860, avgs=0
050/300: dt: 0.9000, rms radial error=167.935, avgs=0
055/300: dt: 0.9000, rms radial error=167.012, avgs=0
060/300: dt: 0.9000, rms radial error=166.092, avgs=0
065/300: dt: 0.9000, rms radial error=165.175, avgs=0
070/300: dt: 0.9000, rms radial error=164.262, avgs=0
075/300: dt: 0.9000, rms radial error=163.352, avgs=0
080/300: dt: 0.9000, rms radial error=162.447, avgs=0
085/300: dt: 0.9000, rms radial error=161.547, avgs=0
090/300: dt: 0.9000, rms radial error=160.651, avgs=0
095/300: dt: 0.9000, rms radial error=159.759, avgs=0
100/300: dt: 0.9000, rms radial error=158.871, avgs=0
105/300: dt: 0.9000, rms radial error=157.989, avgs=0
110/300: dt: 0.9000, rms radial error=157.110, avgs=0
115/300: dt: 0.9000, rms radial error=156.236, avgs=0
120/300: dt: 0.9000, rms radial error=155.367, avgs=0
125/300: dt: 0.9000, rms radial error=154.502, avgs=0
130/300: dt: 0.9000, rms radial error=153.642, avgs=0
135/300: dt: 0.9000, rms radial error=152.786, avgs=0
140/300: dt: 0.9000, rms radial error=151.934, avgs=0
145/300: dt: 0.9000, rms radial error=151.087, avgs=0
150/300: dt: 0.9000, rms radial error=150.245, avgs=0
155/300: dt: 0.9000, rms radial error=149.407, avgs=0
160/300: dt: 0.9000, rms radial error=148.573, avgs=0
165/300: dt: 0.9000, rms radial error=147.744, avgs=0
170/300: dt: 0.9000, rms radial error=146.919, avgs=0
175/300: dt: 0.9000, rms radial error=146.098, avgs=0
180/300: dt: 0.9000, rms radial error=145.282, avgs=0
185/300: dt: 0.9000, rms radial error=144.470, avgs=0
190/300: dt: 0.9000, rms radial error=143.663, avgs=0
195/300: dt: 0.9000, rms radial error=142.860, avgs=0
200/300: dt: 0.9000, rms radial error=142.061, avgs=0
205/300: dt: 0.9000, rms radial error=141.266, avgs=0
210/300: dt: 0.9000, rms radial error=140.476, avgs=0
215/300: dt: 0.9000, rms radial error=139.693, avgs=0
220/300: dt: 0.9000, rms radial error=138.914, avgs=0
225/300: dt: 0.9000, rms radial error=138.140, avgs=0
230/300: dt: 0.9000, rms radial error=137.370, avgs=0
235/300: dt: 0.9000, rms radial error=136.604, avgs=0
240/300: dt: 0.9000, rms radial error=135.842, avgs=0
245/300: dt: 0.9000, rms radial error=135.085, avgs=0
250/300: dt: 0.9000, rms radial error=134.332, avgs=0
255/300: dt: 0.9000, rms radial error=133.583, avgs=0
260/300: dt: 0.9000, rms radial error=132.838, avgs=0
265/300: dt: 0.9000, rms radial error=132.098, avgs=0
270/300: dt: 0.9000, rms radial error=131.362, avgs=0
275/300: dt: 0.9000, rms radial error=130.629, avgs=0
280/300: dt: 0.9000, rms radial error=129.901, avgs=0
285/300: dt: 0.9000, rms radial error=129.177, avgs=0
290/300: dt: 0.9000, rms radial error=128.456, avgs=0
295/300: dt: 0.9000, rms radial error=127.740, avgs=0
300/300: dt: 0.9000, rms radial error=127.028, avgs=0

spherical inflation complete.
.
.
.
epoch 4 (K=1280.0), pass 1, starting sse = 541.21
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.32/19 = 0.01710
finalwriting spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.10 hours
distance error %10.00
.
.
.
pass 1: epoch 1 of 3 starting distance error %21.36
pass 1: epoch 2 of 3 starting distance error %21.04
unfolding complete - removing small folds...
starting distance error %20.80
removing remaining folds...
final distance error %20.81
364: 0 negative triangles
.
.
.


Thanks,

Kenichiro Tanaka.

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Re: [Freesurfer] Mcsrch error during recon-all

2011-09-28 Thread Nick Schmansky

the log does not indicate that mri_em_register exited with an error.  it
appears that it produced its output correctly and continued through to
nearly the end of the stream.  the IFLAG messages can be ignored.

the log indicates that mri_label2label is exiting with an error when
trying to load the label from the fsaverage directory.  the fsaverage
subject is symlinked to the users SUBJECTS_DIR (to save space), but
sometimes this seems to cause problems on some systems.  i would try
copying it to your subjects dir:

cd $SUBJECTS_DIR
rm fsaverage
cp -r $FREESURFER_HOME/subjects/fsaverage .

then you just need to run the last two stages of recon-all:

recon-all -s  -balabels -label-exvivo-ec

or if you dont care about the Brodmann or exvivo EC labels, you dont
need to run anything.

for reference:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

n.


On Wed, 2011-09-28 at 17:36 -0400, Warren Winter wrote:
> Hi Nick,
> 
> 
> Thanks for your help.
> 
> 
> The first set of errors (of the kind I described) follows the command
> " mri_em_register -skull
> nu.mgz 
> /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca
>  transforms/talairach_with_skull.lta "
> 
> 
> The next follows the command " mri_em_register -uns 3 -mask
> brainmask.mgz
> nu.mgz 
> /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_2008-03-26.gca
>  transforms/talairach.lta"
> 
> 
> The next follows the command " mri_em_register -skull -t
> transforms/talairach.lta
> nu_noneck.mgz 
> /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca
>  transforms/talairach_with_skull_2.lta "
> 
> 
> I've attached the log if you could use it for reference.
> 
> 
> Best,
> 
> 
> Warren
> 
> 
> 
> 
> 
> On Sep 28, 2011, at 4:18 PM, Nick Schmansky wrote:
> 
> > the IFLAG messages can be ignored if mri_em_register is not exiting
> > with
> > error.  which command is running that is exiting with error?  can
> > you
> > send that command line from the recon-all.log file?
> > 
> > n.
> > 
> > On Wed, 2011-09-28 at 16:02 -0400, Warren Winter wrote:
> > > Hi,
> > > 
> > > 
> > > Each time I have run recon-all on our subjects, I end up with the
> > > same
> > > slew of error messages underneath "Computing MAP estimate using [x
> > > number of] samples" and underneath "EM alignment process":
> > > 
> > > 
> > > "IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE
> > > MCSRCH
> > > ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR
> > > GRADIENT ARE INCORRECT OR INCORRECT TOLERANCES"
> > > 
> > > 
> > > At the very end of the log file I see:
> > > 
> > > 
> > > "Loading source label.
> > > Abort
> > > Linux rc-twice 2.6.39.2-mosix #1 SMP Wed Jun 29 11:53:08 EDT 2011
> > > x86_64 x86_64 x86_64 GNU/Linux
> > > 
> > > 
> > > recon-all -s 5 exited with ERRORS at Tue Sep 27 03:23:46 EDT 2011"
> > > 
> > > 
> > > Any help on this would be greatly appreciated.
> > > 
> > > 
> > > Best,
> > > 
> > > 
> > > Warren
> > > 
> > > --
> > > Warren Winter
> > > Lab Coordinator
> > > Children's Hospital Boston
> > > Division of Developmental Medicine
> > > 1 Autumn Street, AU 650
> > > Boston, MA 02215
> > > 857-218-5224
> > > 
> > > 
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > 
> > 
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the sender
> > and properly
> > dispose of the e-mail.
> > 
> > 
> 
> 
> --
> Warren Winter
> Lab Coordinator
> Children's Hospital Boston
> Division of Developmental Medicine
> 1 Autumn Street, AU 650
> Boston, MA 02215
> 857-218-5224
> 
> 

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Re: [Freesurfer] Mcsrch error during recon-all

2011-09-28 Thread Nick Schmansky

the IFLAG messages can be ignored if mri_em_register is not exiting with
error.  which command is running that is exiting with error?  can you
send that command line from the recon-all.log file?

n.

On Wed, 2011-09-28 at 16:02 -0400, Warren Winter wrote:
> Hi,
> 
> 
> Each time I have run recon-all on our subjects, I end up with the same
> slew of error messages underneath "Computing MAP estimate using [x
> number of] samples" and underneath "EM alignment process":
> 
> 
> "IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH
> ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR
> GRADIENT ARE INCORRECT OR INCORRECT TOLERANCES"
> 
> 
> At the very end of the log file I see:
> 
> 
> "Loading source label.
> Abort
> Linux rc-twice 2.6.39.2-mosix #1 SMP Wed Jun 29 11:53:08 EDT 2011
> x86_64 x86_64 x86_64 GNU/Linux
> 
> 
> recon-all -s 5 exited with ERRORS at Tue Sep 27 03:23:46 EDT 2011"
> 
> 
> Any help on this would be greatly appreciated.
> 
> 
> Best,
> 
> 
> Warren
> 
> --
> Warren Winter
> Lab Coordinator
> Children's Hospital Boston
> Division of Developmental Medicine
> 1 Autumn Street, AU 650
> Boston, MA 02215
> 857-218-5224
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Mcsrch error during recon-all

2011-09-28 Thread Warren Winter

Hi,

Each time I have run recon-all on our subjects, I end up with the same slew of 
error messages underneath "Computing MAP estimate using [x number of] samples" 
and underneath "EM alignment process":

"IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
INCORRECT OR INCORRECT TOLERANCES"

At the very end of the log file I see:

"Loading source label.
Abort
Linux rc-twice 2.6.39.2-mosix #1 SMP Wed Jun 29 11:53:08 EDT 2011 x86_64 x86_64 
x86_64 GNU/Linux

recon-all -s 5 exited with ERRORS at Tue Sep 27 03:23:46 EDT 2011"

Any help on this would be greatly appreciated.

Best,

Warren

--
Warren Winter
Lab Coordinator
Children's Hospital Boston
Division of Developmental Medicine
1 Autumn Street, AU 650
Boston, MA 02215
857-218-5224

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Re: [Freesurfer] MCSRCH ERROR

2011-08-08 Thread Bruce Fischl

Can you send us e recon-all.log file?



On Aug 8, 2011, at 4:30 AM, "Irwin, William"  wrote:

> Hi-
> 
>  
> 
> I’m at a bit of a loss as to how to address and/or fix these errors.
> 
>  
> 
> The native input images are very good quality; the conversion to T1.mgz is 
> fine; the brainmask.mgz is good, a bit of dura remained at the 
> parietal/occipital region (very common); otherwise, the skull stripping is 
> very clean.
> 
>  
> 
> The recon-all “finished” but with errors as expected. Processing “continued” 
> to the end, but there is no output except in /mri and /touch.
> 
>  
> 
> Doing: #@# Skull Stripping
> 
>  
> 
> First under “Computing MAP estimate using 3481 samples...”
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10327.2 
>  tol 0.10
> 
>  
> 
> Then several of the same under “EM alignment process ...”
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization...
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESpass 4 through quasi-newton minimization...
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESpass 5 through quasi-newton minimization...
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 017: -log(p) = 
> 1145822.4  tol 0.00
> 
>  
> 
> Then again at “Computing MAP estimate using 2772 samples...”
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 7006.0  
> tol 0.10
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
> 
>  
> 
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 
> 838978.4  tol 0.00
> 
>  
> 
> Thanks,
> 
> Wil
> 
>  
> 
> 
> William Irwin | Brain Imaging Coordinator
> UCSF | Memory and Aging Center
> 350 Parnassus Avenue, Suite 905
> San Francisco  CA  94143-1207
> wir...@memory.ucsf.edu | memory.ucsf.edu
> p: 415.476.1680 | f: 415.476.1816
> 
>  
> 
>  
> 
>  
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] MCSRCH ERROR

2011-08-08 Thread Irwin, William

Hi-

I'm at a bit of a loss as to how to address and/or fix these errors.

The native input images are very good quality; the conversion to T1.mgz is 
fine; the brainmask.mgz is good, a bit of dura remained at the 
parietal/occipital region (very common); otherwise, the skull stripping is very 
clean.

The recon-all "finished" but with errors as expected. Processing "continued" to 
the end, but there is no output except in /mri and /touch.

Doing: #@# Skull Stripping

First under "Computing MAP estimate using 3481 samples..."

IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN 
OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR 
INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10327.2  tol 0.10

Then several of the same under "EM alignment process ..."

IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN 
OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR 
INCORRECT TOLERANCESpass 2 through quasi-newton minimization...

IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN 
OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR 
INCORRECT TOLERANCESpass 3 through quasi-newton minimization...

IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN 
OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR 
INCORRECT TOLERANCESpass 4 through quasi-newton minimization...

IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN 
OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR 
INCORRECT TOLERANCESpass 5 through quasi-newton minimization...

IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN 
OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR 
INCORRECT TOLERANCESoutof QuasiNewtonEMA: 017: -log(p) = 1145822.4  tol 0.00

Then again at "Computing MAP estimate using 2772 samples..."

IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN 
OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR 
INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 7006.0  tol 0.10

IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN 
OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR 
INCORRECT TOLERANCESpass 2 through quasi-newton minimization...

IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN 
OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR 
INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 838978.4  tol 0.00

Thanks,
Wil


William Irwin | Brain Imaging Coordinator
UCSF | Memory and Aging Center
350 Parnassus Avenue, Suite 905
San Francisco  CA  94143-1207
wir...@memory.ucsf.edu | memory.ucsf.edu
p: 415.476.1680 | f: 415.476.1816



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Re: [Freesurfer] MCSRCH error

2011-03-16 Thread Bruce Fischl

Hi Jenifer

we see that sometimes too, and it's never clear why. It's from an open 
source minimization function and doesn't usually mean anything bad. Check 
the talairach_with_skull.lta visually and see if it is ok
cheers
Bruce


  On Wed, 16 Mar 2011, Juranek, Jenifer wrote:

> While processing a normal brain through fsv5.0.0, an unfamiliar message 
> popped up in the screen output (see below).
> Any ideas what I should do about this message (anything in particular I 
> should check)?
>
> Many Thanks,
> Jenifer
>
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
> IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 
> 1145193.0  tol 0.00
> final transform:
> 1.386  -0.067   0.094  -63.518;
> 0.088   1.120  -0.108  -0.481;
> -0.131   0.093   0.972  -2.704;
> 0.000   0.000   0.000   1.000;
>
> writing output transformation to transforms/talairach_with_skull.lta...
> registration took 34 minutes and 38 seconds.
>
> mri_watershed -T1 -brain_atlas 
> /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca 
> transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
>
>
> Mode:  T1 normalized volume
> Mode:  Use the information of atlas (default parms, --help for 
> details)
>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

[Freesurfer] MCSRCH error

2011-03-16 Thread Juranek, Jenifer

While processing a normal brain through fsv5.0.0, an unfamiliar message popped 
up in the screen output (see below).
Any ideas what I should do about this message (anything in particular I should 
check)?

Many Thanks,
Jenifer

 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 1145193.0 
 tol 0.00
final transform:
 1.386  -0.067   0.094  -63.518;
 0.088   1.120  -0.108  -0.481;
-0.131   0.093   0.972  -2.704;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull.lta...
registration took 34 minutes and 38 seconds.

 mri_watershed -T1 -brain_atlas 
/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca 
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


Mode:  T1 normalized volume
Mode:  Use the information of atlas (default parms, --help for details)
 

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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] MCSRCH error using sample data (001.mgz and 002.mgz)

[Freesurfer] MCSRCH error using sample data (001.mgz and 002.mgz)

Re: [Freesurfer] MCSRCH ERROR

Re: [Freesurfer] MCSRCH ERROR

Re: [Freesurfer] MCSRCH ERROR

Re: [Freesurfer] MCSRCH ERROR

Re: [Freesurfer] MCSRCH ERROR

Re: [Freesurfer] MCSRCH ERROR

Re: [Freesurfer] MCSRCH ERROR

[Freesurfer] MCSRCH ERROR

Re: [Freesurfer] Mcsrch error during recon-all

Re: [Freesurfer] Mcsrch error during recon-all

[Freesurfer] Mcsrch error during recon-all

Re: [Freesurfer] MCSRCH ERROR

[Freesurfer] MCSRCH ERROR

Re: [Freesurfer] MCSRCH error

[Freesurfer] MCSRCH error

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