Re: [Freesurfer] MCSRCH error using sample data (001.mgz and 002.mgz)
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> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] MCSRCH ERROR
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 ___ 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.
Re: [Freesurfer] MCSRCH ERROR
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 fis...@nmr.mgh.harvard.eduwrote: 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 http://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 ___ 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.
Re: [Freesurfer] MCSRCH ERROR
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 fis...@nmr.mgh.harvard.edu 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 ___ 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.
Re: [Freesurfer] MCSRCH ERROR
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 WIrwin at memory.ucsf.edu 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 ___ 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.
Re: [Freesurfer] MCSRCH ERROR
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 WIrwin at memory.ucsf.edu 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 ___ 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.
Re: [Freesurfer] MCSRCH ERROR
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, 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
[Freesurfer] MCSRCH ERROR
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@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
Re: [Freesurfer] MCSRCH ERROR
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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Mcsrch error during recon-all
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.
Re: [Freesurfer] Mcsrch error during recon-all
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 ___ 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.
Re: [Freesurfer] Mcsrch error during recon-all
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 subjid -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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] MCSRCH ERROR
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 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.
Re: [Freesurfer] MCSRCH ERROR
Can you send us e recon-all.log file? On Aug 8, 2011, at 4:30 AM, Irwin, William wir...@memory.ucsf.edu 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
[Freesurfer] MCSRCH error
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) ___ 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.
Re: [Freesurfer] MCSRCH error
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) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
