can you send us say the first 10 lines of the output? This command runs fine for me on another dataset On Fri, 24 Mar 2017, Almarshad F. wrote:
> the command line exactly is this > > -DQ67SW:~/Downloads/tutorial_data/buckner_data/tutorial_subjs/004/surf$ > mris_make_face_parcellation lh.sphere.reg $FREESURFER_HOME/lib/bem/ic3.tri > ./lh.ic3.annot > > and the output are many lines of this i coundt evevn copy them all > "CTABannotationAtIndex: index -1 was OOB > CTABannotationAtIndex: index -1 was OOB > CTABannotationAtIndex: index -1 was OOB > CTABannotationAtIndex: index -1 was OOB > CTABannotationAtIndex: index -1 was OOB > CTABannotationAtIndex: index -1 was OOB > CTABannotationAtIndex: index -1 was OOB > CTABannotationAtIndex: index -1 was OOB > CTABannotationAtIndex: index -1 was OOB > CTABannotationAtIndex: index -1 was OOB" > > *** Error in `mris_make_face_parcellation': double free or corruption (out): > 0x0000000002f7ad80 *** > ======= Backtrace: ========= > /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7ff2090be7e5] > /lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7ff2090c6e0a] > /lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7ff2090ca98c] > mris_make_face_parcellation[0x41065b] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7ff209067830] > mris_make_face_parcellation[0x40b529] > ======= Memory map: ======== > 00400000-00929000 r-xp 00000000 08:01 3020757 > /home/fatima/Downloads/freesurfer/bin/mris_make_face_parcellation > 00b28000-00b66000 rw-p 00528000 08:01 3020757 > /home/fatima/Downloads/freesurfer/bin/mris_make_face_parcellation > 00b66000-00b78000 rw-p 00000000 00:00 0 > 02470000-07cb6000 rw-p 00000000 00:00 0 > [heap] > 7ff1fc000000-7ff1fc021000 rw-p 00000000 00:00 0 > 7ff1fc021000-7ff200000000 ---p 00000000 00:00 0 > 7ff202566000-7ff20852f000 rw-p 00000000 00:00 0 > 7ff20852f000-7ff208807000 r--p 00000000 08:01 25821537 > /usr/lib/locale/locale-archive > 7ff208807000-7ff208812000 r-xp 00000000 08:01 2234171 > /lib/x86_64-linux-gnu/libnss_files-2.23.so > 7ff208812000-7ff208a11000 ---p 0000b000 08:01 2234171 > /lib/x86_64-linux-gnu/libnss_files-2.23.so > 7ff208a11000-7ff208a12000 r--p 0000a000 08:01 2234171 > /lib/x86_64-linux-gnu/libnss_files-2.23.so > 7ff208a12000-7ff208a13000 rw-p 0000b000 08:01 2234171 > /lib/x86_64-linux-gnu/libnss_files-2.23.so > 7ff208a13000-7ff208a19000 rw-p 00000000 00:00 0 > 7ff208a19000-7ff208a24000 r-xp 00000000 08:01 2234164 > /lib/x86_64-linux-gnu/libnss_nis-2.23.so > 7ff208a24000-7ff208c23000 ---p 0000b000 08:01 2234164 > /lib/x86_64-linux-gnu/libnss_nis-2.23.so > 7ff208c23000-7ff208c24000 r--p 0000a000 08:01 2234164 > /lib/x86_64-linux-gnu/libnss_nis-2.23.so > 7ff208c24000-7ff208c25000 rw-p 0000b000 08:01 2234164 > /lib/x86_64-linux-gnu/libnss_nis-2.23.so > 7ff208c25000-7ff208c3b000 r-xp 00000000 08:01 2234166 > /lib/x86_64-linux-gnu/libnsl-2.23.so > 7ff208c3b000-7ff208e3a000 ---p 00016000 08:01 2234166 > /lib/x86_64-linux-gnu/libnsl-2.23.so > 7ff208e3a000-7ff208e3b000 r--p 00015000 08:01 2234166 > /lib/x86_64-linux-gnu/libnsl-2.23.so > 7ff208e3b000-7ff208e3c000 rw-p 00016000 08:01 2234166 > /lib/x86_64-linux-gnu/libnsl-2.23.so > 7ff208e3c000-7ff208e3e000 rw-p 00000000 00:00 0 > 7ff208e3e000-7ff208e46000 r-xp 00000000 08:01 2234173 > /lib/x86_64-linux-gnu/libnss_compat-2.23.so > 7ff208e46000-7ff209045000 ---p 00008000 08:01 2234173 > /lib/x86_64-linux-gnu/libnss_compat-2.23.so > 7ff209045000-7ff209046000 r--p 00007000 08:01 2234173 > /lib/x86_64-linux-gnu/libnss_compat-2.23.so > 7ff209046000-7ff209047000 rw-p 00008000 08:01 2234173 > /lib/x86_64-linux-gnu/libnss_compat-2.23.so > 7ff209047000-7ff209206000 r-xp 00000000 08:01 2234167 > /lib/x86_64-linux-gnu/libc-2.23.so > 7ff209206000-7ff209406000 ---p 001bf000 08:01 2234167 > /lib/x86_64-linux-gnu/libc-2.23.so > 7ff209406000-7ff20940a000 r--p 001bf000 08:01 2234167 > /lib/x86_64-linux-gnu/libc-2.23.so > 7ff20940a000-7ff20940c000 rw-p 001c3000 08:01 2234167 > /lib/x86_64-linux-gnu/libc-2.23.so > 7ff20940c000-7ff209410000 rw-p 00000000 00:00 0 > 7ff209410000-7ff209426000 r-xp 00000000 08:01 2232765 > /lib/x86_64-linux-gnu/libgcc_s.so.1 > 7ff209426000-7ff209625000 ---p 00016000 08:01 2232765 > /lib/x86_64-linux-gnu/libgcc_s.so.1 > 7ff209625000-7ff209626000 rw-p 00015000 08:01 2232765 > /lib/x86_64-linux-gnu/libgcc_s.so.1 > 7ff209626000-7ff209647000 r-xp 00000000 08:01 25829649 > /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 > 7ff209647000-7ff209846000 ---p 00021000 08:01 25829649 > /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 > 7ff209846000-7ff209847000 r--p 00020000 08:01 25829649 > /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 > 7ff209847000-7ff209848000 rw-p 00021000 08:01 25829649 > /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 > 7ff209848000-7ff209950000 r-xp 00000000 08:01 2234165 > /lib/x86_64-linux-gnu/libm-2.23.so > 7ff209950000-7ff209b4f000 ---p 00108000 08:01 2234165 > /lib/x86_64-linux-gnu/libm-2.23.so > 7ff209b4f000-7ff209b50000 r--p 00107000 08:01 2234165 > /lib/x86_64-linux-gnu/libm-2.23.so > 7ff209b50000-7ff209b51000 rw-p 00108000 08:01 2234165 > /lib/x86_64-linux-gnu/libm-2.23.so > 7ff209b51000-7ff209cc3000 r-xp 00000000 08:01 25830265 > /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 > 7ff209cc3000-7ff209ec3000 ---p 00172000 08:01 25830265 > /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 > 7ff209ec3000-7ff209ecd000 r--p 00172000 08:01 25830265 > /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 > 7ff209ecd000-7ff209ecf000 rw-p 0017c000 08:01 25830265 > /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 > 7ff209ecf000-7ff209ed3000 rw-p 00000000 00:00 0 > 7ff209ed3000-7ff209eeb000 r-xp 00000000 08:01 2234178 > /lib/x86_64-linux-gnu/libpthread-2.23.so > 7ff209eeb000-7ff20a0ea000 ---p 00018000 08:01 2234178 > /lib/x86_64-linux-gnu/libpthread-2.23.so > 7ff20a0ea000-7ff20a0eb000 r--p 00017000 08:01 2234178 > /lib/x86_64-linux-gnu/libpthread-2.23.so > 7ff20a0eb000-7ff20a0ec000 rw-p 00018000 08:01 2234178 > /lib/x86_64-linux-gnu/libpthread-2.23.so > 7ff20a0ec000-7ff20a0f0000 rw-p 00000000 00:00 0 > 7ff20a0f0000-7ff20a0f3000 r-xp 00000000 08:01 2234163 > /lib/x86_64-linux-gnu/libdl-2.23.so > 7ff20a0f3000-7ff20a2f2000 ---p 00003000 08:01 2234163 > /lib/x86_64-linux-gnu/libdl-2.23.so > 7ff20a2f2000-7ff20a2f3000 r--p 00002000 08:01 2234163 > /lib/x86_64-linux-gnu/libdl-2.23.so > 7ff20a2f3000-7ff20a2f4000 rw-p 00003000 08:01 2234163 > /lib/x86_64-linux-gnu/libdl-2.23.so > 7ff20a2f4000-7ff20a2fd000 r-xp 00000000 08:01 2234182 > /lib/x86_64-linux-gnu/libcrypt-2.23.so > 7ff20a2fd000-7ff20a4fc000 ---p 00009000 08:01 2234182 > /lib/x86_64-linux-gnu/libcrypt-2.23.so > 7ff20a4fc000-7ff20a4fd000 r--p 00008000 08:01 2234182 > /lib/x86_64-linux-gnu/libcrypt-2.23.so > 7ff20a4fd000-7ff20a4fe000 rw-p 00009000 08:01 2234182 > /lib/x86_64-linux-gnu/libcrypt-2.23.so > 7ff20a4fe000-7ff20a52c000 rw-p 00000000 00:00 0 > 7ff20a52c000-7ff20a545000 r-xp 00000000 08:01 2232918 > /lib/x86_64-linux-gnu/libz.so.1.2.8 > 7ff20a545000-7ff20a744000 ---p 00019000 08:01 2232918 > /lib/x86_64-linux-gnu/libz.so.1.2.8 > 7ff20a744000-7ff20a745000 r--p 00018000 08:01 2232918 > /lib/x86_64-linux-gnu/libz.so.1.2.8 > 7ff20a745000-7ff20a746000 rw-p 00019000 08:01 2232918 > /lib/x86_64-linux-gnu/libz.so.1.2.8 > 7ff20a746000-7ff20a76c000 r-xp 00000000 08:01 2234168 > /lib/x86_64-linux-gnu/ld-2.23.so > 7ff20a949000-7ff20a951000 rw-p 00000000 00:00 0 > 7ff20a968000-7ff20a96b000 rw-p 00000000 00:00 0 > 7ff20a96b000-7ff20a96c000 r--p 00025000 08:01 2234168 > /lib/x86_64-linux-gnu/ld-2.23.so > 7ff20a96c000-7ff20a96d000 rw-p 00026000 08:01 2234168 > /lib/x86_64-linux-gnu/ld-2.23.so > 7ff20a96d000-7ff20a96e000 rw-p 00000000 00:00 0 > 7ffc1ff2c000-7ffc20087000 rw-p 00000000 00:00 0 > [stack] > 7ffc200df000-7ffc200e1000 r--p 00000000 00:00 0 > [vvar] > 7ffc200e1000-7ffc200e3000 r-xp 00000000 00:00 0 > [vdso] > ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 > [vsyscall] > Aborted (core dumped) > fatima@fatima-DQ67SW:~/Downloads/tutorial_data/buckner_data/tutorial_subjs/004/surf$ > cd ~ > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Friday, March 24, 2017 5:48 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] error with mris_make_face_parcellation > > can you just send it as text? Screen shots are not nearly as useful for > us > On Fri, 24 Mar 2017, Almarshad F. wrote: > >> i attached a screen shot of the command and the output >> >> >> mris_make_face_parcellation lh.sphere.reg $FREESURFER_HOME/lib/bem/ic3.tri >> ./lh.ic3.annot > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, March 24, 2017 6:07 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] error with mris_make_face_parcellation > > can you send the command line and the terminal output as plain text in > the email? > > > On 3/24/17 1:50 PM, Almarshad F. wrote: >> ~/Downloads/tutorial_data/buckner_data/tutorial_subjs/004/surf$ >> mris_make_face_parcellation lh.sphere.reg $FREESURFER_HOME/lib/bem/ic3.tri >> ./lh.ic3.annot >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Friday, March 24, 2017 5:48 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] error with mris_make_face_parcellation >> >> can you just send it as text? Screen shots are not nearly as useful for >> us >> On Fri, 24 Mar 2017, Almarshad F. wrote: >> >>> i attached a screen shot of the command and the output >>> >>> >>> mris_make_face_parcellation lh.sphere.reg $FREESURFER_HOME/lib/bem/ic3.tri >>> ./lh.ic3.annot >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Friday, March 24, 2017 5:15 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] error with mris_make_face_parcellation >>> >>> can you please send your complete command line and all screen output? >>> >>> thanks >>> Bruce >>> On >>> Fri, 24 Mar 2017, Almarshad F. wrote: >>> >>>> With the ?h.sphere it gives the message (INFO: CATBunique( ) could not find >>>> a unique set in 100 tries) ! >>>> >>>> >>>> >>>> >>>> >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve >>>> Sent: 24 March 2017 16:20 >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] error with mris_make_face_parcellation >>>> >>>> >>>> >>>> what are you using as lh.surf? It should be ?h.sphere or ?h.sphere.reg >>>> >>>> >>>> >>>> On 3/24/17 12:12 PM, Almarshad F. wrote: >>>> >>>> Hi freesurfer's experts; >>>> >>>> >>>> >>>> >>>> >>>> I was trying to use mris_make_face_parcellation lh.surf >>>> $FREESURFER_HOME/lib >>>> /bem/ic3.tri ./lh.ic3.annot to generate uniform-sized parcellation .. >>>> >>>> >>>> >>>> but i get the following error >>>> >>>> >>>> >>>> >>>> >>>> *** Error in `mris_make_face_parcellation': double free or corruption >>>> (out): >>>> 0x0000000003fec560 *** >>>> >>>> ======= Backtrace: ========= >>>> >>>> /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f96d00ef7e5] >>>> >>>> /lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7f96d00f7e0a] >>>> >>>> /lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f96d00fb98c] >>>> >>>> mris_make_face_parcellation[0x41065b] >>>> >>>> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f96d0098830] >>>> >>>> mris_make_face_parcellation[0x40b529] >>>> >>>> >>>> >>>> i also attached the log file >>>> >>>> >>>> >>>> kidest regards, >>>> >>>> fatima >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> >>>> 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 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 > > _______________________________________________ > 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
