Hi Eli, the -make all flag contains a bug in the 6.0 release. This can be fixed if you download this script - ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/recon-all.makefile - and overwrite the current $FREESURFER_HOME/bin/recon-all.makefile
Let me know if you still have issues
best, Andrew
On 7/31/18, 3:15 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
hmmmm, maybe -make all has changed (or my memory of what it does is incorrect). I'll find someone else here to help you out
cheers Bruce On Tue, 31 Jul 2018, Bruce Fischl wrote:
> did you run > > recon-all -s <subject name> -make all > > ? > > > I don't see it in the log > On Tue, 31 Jul 2018, Rockers, Elijah D. wrote: > >> >> External Email - Use Caution >> >> Oh, yep, sorry about that. I copy the list on this e-mail, and attach the >> log. I think the list >> blocks attachments, but if anyone wants to see full log I can send it. >> >> >> Thanks to all, >> >> -Eli >> >> ____________________________________________________________________________________________________ >> From: Bruce Fischl fischl@nmr.mgh.harvard.edu >> Sent: Tuesday, July 31, 2018 2:03:05 PM >> To: Rockers, Elijah D. >> Subject: Re: Surface editing: recon-all exited with errors >> can you cc the list on these emails so others can help? >> On Tue, 31 Jul 2018, >> Rockers, Elijah D. wrote: >> >> > >> > External Email - Use Caution >> > >> > The recon-all -make all command finished relatively quickly, still with >> > errors. It's still showing >> > the same errors, and I have attached the new recon-all.log. >> > >> > ___________________________________________________________________________________________________ >> _ >> > From: Rockers, Elijah D. >> > Sent: Tuesday, July 31, 2018 12:32:11 PM >> > To: Bruce Fischl >> > Subject: Re: Surface editing: recon-all exited with errors >> > >> > Odd. I assumed the individual recon-all commands in the log are just >> > what is reported by the >> general >> > pipeline, since I definitely did not issue all those commands >> > separately. I just used the >> recon-all >> > -make all command after editing. In anycase, I will run it again to see >> > if anything changes, but I >> > think that would be surprising. >> > >> > >> > Thanks again >> > >> > - Eli >> > >> > ___________________________________________________________________________________________________ >> _ >> > From: Bruce Fischl fischl@nmr.mgh.harvard.edu >> > Sent: Tuesday, July 31, 2018 11:52:59 AM >> > To: Rockers, Elijah D. >> > Subject: Re: Surface editing: recon-all exited with errors >> > Hi Eli >> > >> > it's hard for me to tell since you have so many individual recon-all >> > commands, but it looks like you didn't recreate all the surfaces after >> > editing. Errors like thiss one: >> > >> > mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn't match >> > ../surf/lh.white.preaparc >> > >> > typically mean something hasn't been recreated properly. Try running >> > recon-all -make all >> > >> > cheers >> > Bruce >> > >> > >> > On Tue, >> > 31 Jul 2018, Rockers, Elijah D. wrote: >> > >> > > >> > > External Email - Use Caution >> > > >> > > Hi Bruce, >> > > >> > > >> > > I have attached the recon-all.log, regarding an exit with ERRORS that >> > > occured after manually >> > editing >> > > the surface. Thanks for taking a look. >> > > >> > > >> > > Also, I double checked - the original recon-all command finished with >> > > no errors. So it seems the >> > > message occurs after surface editing. But the new reconstructed >> > > surfaces appear accurate, at >> least >> > > with respect to gray and white matter boundaries. Let me know if >> > > there's anything else you need. >> > > >> > > >> > > Thanks again, >> > > >> > > - Eli >> > > >> > > Houston Methodist. Leading Medicine. >> > > >> > > Houston Methodist is ranked by U.S. News & World Report as the No. 1 >> > > hospital in Texas for >> patient >> > > care. Houston Methodist is nationally ranked in 8 specialties and is >> > > designated as a Magnet >> > hospital >> > > for excellence in nursing. Visit us at http://houstonmethodist.org. >> > > Follow >> > > usathttps://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHos... >> xE >> > jkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ds98HqtzhWqTZ4zNG >> >> > seN-axVe5fM_ZPQ9W9OHoSzLLo&s=5CE2NSVpAt16S_bmsgO_Okvmb5bkLvXMIjkxSTQ2C5g&e= >> > > andhttps://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_HoustonMeth... >> tDi >> > FixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ds98HqtzhWqTZ >> >> > 4zNGseN-axVe5fM_ZPQ9W9OHoSzLLo&s=1x_6X2u7_1TSprfJDQX2_pJs3OEQcXqNYjVB7pVhpzE&e=. >> > > >> > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston >> > > Methodist and/or its >> relevant >> > > affiliates and may contain restricted and privileged material for the >> > > sole use of the intended >> > > recipient(s). Any review, use, distribution or disclosure by others is >> > > strictly prohibited. If >> you >> > > are not the intended recipient (or authorized to receive for the >> > > recipient), please contact the >> > > sender and delete all copies of the message. Thank you. >> > > >> > > >> > > >> > >> > >> > 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 >> > https: //urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIFAw&c=QmPt >> >> > DiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ds98HqtzhWq >> >> > TZ4zNGseN-axVe5fM_ZPQ9W9OHoSzLLo&s=xCXJrzgzXHHAcYBpjDRMUejaZuRv3TRvaTInF4j-rTw&e= >> > . 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. >> > >> > Houston Methodist. Leading Medicine. >> > >> > Houston Methodist is ranked by U.S. News & World Report as the No. 1 >> > hospital in Texas for patient >> > care. Houston Methodist is nationally ranked in 8 specialties and is >> > designated as a Magnet >> hospital >> > for excellence in nursing. Visit us at http://houstonmethodist.org. >> > Follow us >> > athttps://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHos... >> jkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=v8b-fopH40l9QFjmU >> UagXcSud1KidLOGC6r-yJIaMgs&s=n10KnHWoZmKWhUnIST22Wd_-CpO6CKEhs_Px28LwPgA&e= >> > andhttps://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_HoustonMeth... >> FixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=v8b-fopH40l9Q >> FjmUUagXcSud1KidLOGC6r-yJIaMgs&s=GwxcOWoaL8fedVWq0c-38F-3JnNPyXb_RB7i0S5ceqM&e=. >> > >> > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston >> > Methodist and/or its relevant >> > affiliates and may contain restricted and privileged material for the >> > sole use of the intended >> > recipient(s). Any review, use, distribution or disclosure by others is >> > strictly prohibited. If you >> > are not the intended recipient (or authorized to receive for the >> > recipient), please contact the >> > sender and delete all copies of the message. Thank you. >> > >> > >> > >> >> >> 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 >> https: //urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIFbA&c=QmPt >> DiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=v8b-fopH40l >> 9QFjmUUagXcSud1KidLOGC6r-yJIaMgs&s=A0SZGR2sDIg_jnaRfyaqVBWfrNkK2oR3NjXd7PNgtAQ&e= >> . 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. >> >> Houston Methodist. Leading Medicine. >> >> Houston Methodist is ranked by U.S. News & World Report as the No. 1 >> hospital in Texas for patient >> care. Houston Methodist is nationally ranked in 8 specialties and is >> designated as a Magnet hospital >> for excellence in nursing. Visit us at houstonmethodist.org. Follow us at >> twitter.com/MethodistHosp >> and facebook.com/HoustonMethodist. >> >> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston >> Methodist and/or its relevant >> affiliates and may contain restricted and privileged material for the sole >> use of the intended >> recipient(s). Any review, use, distribution or disclosure by others is >> strictly prohibited. If you >> are not the intended recipient (or authorized to receive for the >> recipient), please contact the >> sender and delete all copies of the message. Thank you. >> >> >> >