Dear Pedro Paulo:
I need to continue the freesurfer professing from a specific stage of autorecon2 (careginv; stage 4 of autorecon2 in http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllStableTablev4)..
Which is the command line to do it ?...
Sincerely,
Gonzalo Rojas Costa
It would be: recon-all -s YOUR_SUBJ -make all ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business
2009/7/22 Gonzalo Rojas Costa grojasy@puc.cl
Dear Pedro Paulo:
I need to continue the freesurfer professing from a specific stage of autorecon2 (careginv; stage 4 of autorecon2 in http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllStableTablev4)..
Which is the command line to do it ?...
Sincerely,
Gonzalo Rojas Costa
Dear Pedro Paulo:
I got the following error when I processing the autorecon2 stage...
" 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 187 187 45 251 CC_Posterior 540 540 46 252 CC_Mid_Posterior 182 182 47 253 CC_Central 131 131 48 254 CC_Mid_Anterior 162 162 49 255 CC_Anterior 219 219
Reporting on 49 segmentations #-------------------------------------------- #@# Cortical ribbon mask Fri Jul 24 04:47:12 CLT 2009 /home/image/bin/freesurfer/subjects/rezende/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance rezende
mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux ubuntu 2.6.27-7-generic #1 SMP Fri Oct 24 06:42:44 UTC 2008 i686 GNU/Linux
recon-all exited with ERRORS at Fri Jul 24 04:47:15 CLT 2009"
Which is the problem ?... How can install libtiff.so.3 ?..
Sincerely,
Gonzalo Rojas Costa
Hi
On Ubuntu, you will need to do the following: cd /usr/lib sudo ln -s libtiff.so.4 libtiff.so.3 ( from http://surfer.nmr.mgh.harvard.edu/fswiki/Download )
The second command only works if you have write access to /usr/lib.. otherwise you could contact your sysadmin.
Krish
On Jul 24, 2009, at 11:15 AM, Gonzalo Rojas Costa wrote:
Dear Pedro Paulo:
I got the following error when I processing the autorecon2 stage...
" 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 187 187 45 251 CC_Posterior 540 540 46 252 CC_Mid_Posterior 182 182 47 253 CC_Central 131 131 48 254 CC_Mid_Anterior 162 162 49 255 CC_Anterior 219 219
Reporting on 49 segmentations #-------------------------------------------- #@# Cortical ribbon mask Fri Jul 24 04:47:12 CLT 2009 /home/image/bin/freesurfer/subjects/rezende/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3 -- label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance rezende
mris_volmask.bin: error while loading shared libraries: libtiff.so. 3: cannot open shared object file: No such file or directory Linux ubuntu 2.6.27-7-generic #1 SMP Fri Oct 24 06:42:44 UTC 2008 i686 GNU/Linux
recon-all exited with ERRORS at Fri Jul 24 04:47:15 CLT 2009"
Which is the problem ?... How can install libtiff.so.3 ?..
Sincerely,
Gonzalo Rojas Costa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi:
But the sysadmin forgot the password of the superuser... I created the link in the /home/image directory, and in /home/image/freesurfer/bin, but freesurfer didn't find the lib... How can I solve the problem... How can I specify to freesurfer that the lib is in another folder ?... Any idea ?...
SIncerely,
Gonzalo Rojas Costa
Krish Subramaniam escribió:
Hi
On Ubuntu, you will need to do the following: cd /usr/lib sudo ln -s libtiff.so.4 libtiff.so.3 ( from http://surfer.nmr.mgh.harvard.edu/fswiki/Download )
The second command only works if you have write access to /usr/lib.. otherwise you could contact your sysadmin.
Krish
On Jul 24, 2009, at 11:15 AM, Gonzalo Rojas Costa wrote:
Dear Pedro Paulo:
I got the following error when I processing the autorecon2 stage...
" 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 187 187 45 251 CC_Posterior 540 540 46 252 CC_Mid_Posterior 182 182 47 253 CC_Central 131 131 48 254 CC_Mid_Anterior 162 162 49 255 CC_Anterior 219 219
Reporting on 49 segmentations #-------------------------------------------- #@# Cortical ribbon mask Fri Jul 24 04:47:12 CLT 2009 /home/image/bin/freesurfer/subjects/rezende/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3 -- label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance rezende
mris_volmask.bin: error while loading shared libraries: libtiff.so. 3: cannot open shared object file: No such file or directory Linux ubuntu 2.6.27-7-generic #1 SMP Fri Oct 24 06:42:44 UTC 2008 i686 GNU/Linux
recon-all exited with ERRORS at Fri Jul 24 04:47:15 CLT 2009"
Which is the problem ?... How can install libtiff.so.3 ?..
Sincerely,
Gonzalo Rojas Costa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I believe the following might work
- create a symbolic link to libtiff.so.4 in your home directory like
cd /home/image/freesurfer/lib/ ln -s /usr/lib/libtiff.so.4 libtiff.so.3
- add this to your LD_LIBRARY_PATH.. first you need to check your LD_LIBRARY_PATH is already defined.
echo $LD_LIBRARY_PATH
* if this says undefined variable, do this
setenv LD_LIBRARY_PATH /home/image/freesurfer/lib
* if it's already defined
setenv LD_LIBRARY_PATH /home/image/freesurfer/lib:${LD_LIBRARY_PATH}
and try.
If it works you should take these to your ~/.cshrc where they are defined everytime
Krish
On Jul 24, 2009, at 11:38 AM, Gonzalo Rojas Costa wrote:
Hi:
But the sysadmin forgot the password of the superuser... I created the link in the /home/image directory, and in /home/image/freesurfer/bin, but freesurfer didn't find the lib... How can I solve the problem... How can I specify to freesurfer that the lib is in another folder ?... Any idea ?...
SIncerely,
Gonzalo Rojas Costa
Krish Subramaniam escribió:
Hi
On Ubuntu, you will need to do the following: cd /usr/lib sudo ln -s libtiff.so.4 libtiff.so.3 ( from http://surfer.nmr.mgh.harvard.edu/fswiki/Download )
The second command only works if you have write access to /usr/lib.. otherwise you could contact your sysadmin.
Krish
On Jul 24, 2009, at 11:15 AM, Gonzalo Rojas Costa wrote:
Dear Pedro Paulo:
I got the following error when I processing the autorecon2 stage...
" 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 187 187 45 251 CC_Posterior 540 540 46 252 CC_Mid_Posterior 182 182 47 253 CC_Central 131 131 48 254 CC_Mid_Anterior 162 162 49 255 CC_Anterior 219 219
Reporting on 49 segmentations #-------------------------------------------- #@# Cortical ribbon mask Fri Jul 24 04:47:12 CLT 2009 /home/image/bin/freesurfer/subjects/rezende/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3 -- label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance rezende
mris_volmask.bin: error while loading shared libraries: libtiff.so. 3: cannot open shared object file: No such file or directory Linux ubuntu 2.6.27-7-generic #1 SMP Fri Oct 24 06:42:44 UTC 2008 i686 GNU/Linux
recon-all exited with ERRORS at Fri Jul 24 04:47:15 CLT 2009"
Which is the problem ?... How can install libtiff.so.3 ?..
Sincerely,
Gonzalo Rojas Costa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
I think if he forgot the root password there's no way to do this ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business
2009/7/24 Gonzalo Rojas Costa grojasy@puc.cl
Hi:
But the sysadmin forgot the password of the superuser... I created the link in the /home/image directory, and in /home/image/freesurfer/bin, but freesurfer didn't find the lib... How can I solve the problem... How can I specify to freesurfer that the lib is in another folder ?... Any idea ?...
SIncerely,
Gonzalo Rojas Costa
Krish Subramaniam escribió:
Hi
On Ubuntu, you will need to do the following: cd /usr/lib sudo ln -s libtiff.so.4 libtiff.so.3 ( from http://surfer.nmr.mgh.harvard.edu/fswiki/Download )
The second command only works if you have write access to /usr/lib.. otherwise you could contact your sysadmin.
Krish
On Jul 24, 2009, at 11:15 AM, Gonzalo Rojas Costa wrote:
Dear Pedro Paulo:
I got the following error when I processing the autorecon2 stage...
" 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 187 187 45 251 CC_Posterior 540 540 46 252 CC_Mid_Posterior 182 182 47 253 CC_Central 131 131 48 254 CC_Mid_Anterior 162 162 49 255 CC_Anterior 219 219
Reporting on 49 segmentations #-------------------------------------------- #@# Cortical ribbon mask Fri Jul 24 04:47:12 CLT 2009 /home/image/bin/freesurfer/subjects/rezende/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3 -- label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance rezende
mris_volmask.bin: error while loading shared libraries: libtiff.so. 3: cannot open shared object file: No such file or directory Linux ubuntu 2.6.27-7-generic #1 SMP Fri Oct 24 06:42:44 UTC 2008 i686 GNU/Linux
recon-all exited with ERRORS at Fri Jul 24 04:47:15 CLT 2009"
Which is the problem ?... How can install libtiff.so.3 ?..
Sincerely,
Gonzalo Rojas Costa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Hy,
Pedro Paulo de Magalhães Oliveira Junior wrote:
I think if he forgot the root password there's no way to do this
For sure is it possible. He only has to regain root access if the superuser password has been lost in space!
2009/7/24 Gonzalo Rojas Costa <grojasy@puc.cl mailto:grojasy@puc.cl> But the sysadmin forgot the password of the superuser... I created the link in the /home/image directory, and in /home/image/freesurfer/bin, but freesurfer didn't find the lib... How can I solve the problem... How can I specify to freesurfer that the lib is in another folder ?... Any idea ?...
Just use a live CD of the distro of your choice (After booting: mount the system partition of your local installation, chroot to it and use passwd to set the password of root). Or you can boot into single user mode and reset the root password. http://www.google.com/#hl=en&q=linux+root+password+reset should get you further.
I would really recommend to regain root access as you need it also to e.g. maintain your system with updates or to reconfigure your graphic settings.
Bye
Dirk
freesurfer@nmr.mgh.harvard.edu
-
Dirk Dettmering -
Gonzalo Rojas Costa -
Krish Subramaniam -
Pedro Paulo de Magalhães Oliveira Junior