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
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
With the ?h.sphere it gives the message (INFO: CATBunique( ) could not find a unique set in 100 tries) !
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 $FREESURFER_HOME/lib /bem/ic3.tri ./lh.ic3.annot to generate uniform-sized parcellation ..
but i get the following error
*** Error in `mris_make_face_parcellation': double free or corruption (out): 0x0000000003fec560 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f96d00ef7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7f96d00f7e0a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f96d00fb98c]
mris_make_face_parcellation[0x41065b]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f96d0098830]
mris_make_face_parcellation[0x40b529]
i also attached the log file
kidest regards,
fatima
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
~/Downloads/tutorial_data/buckner_data/tutorial_subjs/004/surf$ mris_make_face_parcellation lh.sphere.reg $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 $FREESURFER_HOME/lib /bem/ic3.tri ./lh.ic3.annot to generate uniform-sized parcellation ..
but i get the following error
*** Error in `mris_make_face_parcellation': double free or corruption (out): 0x0000000003fec560 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f96d00ef7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7f96d00f7e0a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f96d00fb98c]
mris_make_face_parcellation[0x41065b]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f96d0098830]
mris_make_face_parcellation[0x40b529]
i also attached the log file
kidest regards,
fatima
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
can you send the command line and the terminal output as plain text in the email?
On 3/24/17 1:50 PM, Almarshad F. wrote:
~/Downloads/tutorial_data/buckner_data/tutorial_subjs/004/surf$ mris_make_face_parcellation lh.sphere.reg $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 $FREESURFER_HOME/lib /bem/ic3.tri ./lh.ic3.annot to generate uniform-sized parcellation ..
but i get the following error
*** Error in `mris_make_face_parcellation': double free or corruption (out): 0x0000000003fec560 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f96d00ef7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7f96d00f7e0a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f96d00fb98c]
mris_make_face_parcellation[0x41065b]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f96d0098830]
mris_make_face_parcellation[0x40b529]
i also attached the log file
kidest regards,
fatima
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
the command line exactly is this
-DQ67SW:~/Downloads/tutorial_data/buckner_data/tutorial_subjs/004/surf$ 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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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 $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, March 24, 2017 6:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error with mris_make_face_parcellation
can you send the command line and the terminal output as plain text in the email?
On 3/24/17 1:50 PM, Almarshad F. wrote:
~/Downloads/tutorial_data/buckner_data/tutorial_subjs/004/surf$ mris_make_face_parcellation lh.sphere.reg $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 $FREESURFER_HOME/lib /bem/ic3.tri ./lh.ic3.annot to generate uniform-sized parcellation ..
but i get the following error
*** Error in `mris_make_face_parcellation': double free or corruption (out): 0x0000000003fec560 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f96d00ef7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7f96d00f7e0a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f96d00fb98c]
mris_make_face_parcellation[0x41065b]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f96d0098830]
mris_make_face_parcellation[0x40b529]
i also attached the log file
kidest regards,
fatima
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can you send us say the first 10 lines of the output? This command runs fine for me on another dataset On Fri, 24 Mar 2017, Almarshad F. wrote:
the command line exactly is this
-DQ67SW:~/Downloads/tutorial_data/buckner_data/tutorial_subjs/004/surf$ 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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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 $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, March 24, 2017 6:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error with mris_make_face_parcellation
can you send the command line and the terminal output as plain text in the email?
On 3/24/17 1:50 PM, Almarshad F. wrote:
~/Downloads/tutorial_data/buckner_data/tutorial_subjs/004/surf$ mris_make_face_parcellation lh.sphere.reg $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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
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Everything just disappear and the first line that I can see is this
CTABannotationAtIndex: index -1 was OOB
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 24 March 2017 18:20 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error with mris_make_face_parcellation
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_s ubjs/004/surf$ cd ~ ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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 $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, March 24, 2017 6:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error with mris_make_face_parcellation
can you send the command line and the terminal output as plain text in the email?
On 3/24/17 1:50 PM, Almarshad F. wrote:
~/Downloads/tutorial_data/buckner_data/tutorial_subjs/004/surf$ mris_make_face_parcellation lh.sphere.reg $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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)[0x7f96d0098 830]
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
freesurfer@nmr.mgh.harvard.edu
-
Almarshad F. -
Bruce Fischl -
Douglas Greve