External Email - Use Caution
Then installing libncurses5-dev doesn't seem like the solution we've been seeking after all. Could you try this instead?
sudo ln -s /usr/lib/x86_64-linux-gnu/libncurses.so.6.2 /usr/lib/x86_64-linux-gnu/libncurses.so.5
Regards, Horsng
On Mar 4, 2021, at 2:17 PM, Ishi Tandon AIB, Jaipur ishi.tandon@student.amity.edu wrote:
External Email - Use CautionUpon running sudo apt-get install libncurses5-dev. This is what I get (attached below).
On Thu, Mar 4, 2021 at 10:36 AM Horsng Junn <hsjunn@gmail.com mailto:hsjunn@gmail.com> wrote: External Email - Use Caution
Hi Ishi,
The results suggest that libncurses5-dev isn't installed at all. (Listed files are all from the default libncurses 6)
In your previous mail you said that:
Also, I have tried sudo apt-get install libncurses5-dev. But that doesn't seem to resolve the issue.
What exactly happened when you ran that command? Could you please re-run that command and attach the result?
Best, Horsng
On Mar 4, 2021, at 1:58 PM, Ishi Tandon AIB, Jaipur <ishi.tandon@student.amity.edu mailto:ishi.tandon@student.amity.edu> wrote:
External Email - Use CautionHello,
Thanks for your response.
I tried to look for libncurses5-dev in my home directory. It appears to be installed on usr/share/doc. Upon checking its permissions, it seemed to be owned by the root.
Also, upon running the aforementioned commands this is what I get (attached below).
On Thu, Mar 4, 2021 at 6:30 AM Horsng Junn <hsjunn@gmail.com mailto:hsjunn@gmail.com> wrote: External Email - Use Caution
Hi Ishi,
Following are what I gathered:
- You're running Freesurfer 7.1.1 on an ubuntu 20.04 box
- Ubuntu 20.04 has libncurses 6 installed as default
- Freesurfer 7.1.1 is linked against libncurses 5
- So previously you were advised to install libncurses5-dev
- And you followed the advice
- But somehow your ubuntu is failing to find the shared object file of that library
It seems your installation of libncurses5-dev is somehow hosed. Could you please double check if libncurses5-dev is successfully installed by running the following commands one at a time? (You don't need to be root to run them.)
apt list --installed *ncurses* find /lib -name 'libncurses*' find /usr/lib -name 'libncurses*' find /usr/local/lib -name 'libncurses*'
Best Horsng
On Mar 3, 2021, at 1:53 PM, Ishi Tandon AIB, Jaipur <ishi.tandon@student.amity.edu mailto:ishi.tandon@student.amity.edu> wrote:
External Email - Use CautionHello experts,
With reference to my previous email, I am attaching the log file of segmentHA_T1.sh https://secure-web.cisco.com/17koz8UN2RKBVc_PKRfYvND1UVHZXxTKzmLbEFHPipI2EJSvpjCuRzZV_c7fp6VPtlTG9z8qYIyTvIhZ8w9rC9tdLMbAnaZ3zC6ey9nF9DpIJZs4LwBOtqsMbub7G28v98LAoZu3GOQ_Lcwof5gutgtANS9J82rQp1ACHgVN23ZVXrQQLRV2RsNwnlNoiEOO_lU96VXgGV0AafEMZEW6dRWadbdMQF4NUDYIML2h2WPxUN92Fmdc0Wp3pJ4J7Xr0EyKu_nQ_ZUctqlUu1buS7uQ/https%3A%2F%2Fsgnldrp.live%2Fclick%3Fredirect%3Dhttp%253A%252F%252FsegmentHA_T1.sh%26dID%3D1614747192045%26linkName%3DsegmentHA_T1.sh bert command.
Please provide your feedback.
Thanks in advance. On Mon, Mar 1, 2021 at 11:03 AM Ishi Tandon AIB, Jaipur <ishi.tandon@student.amity.edu mailto:ishi.tandon@student.amity.edu> wrote: Hello experts,
The recon-all command executed without any errors.
However, on following the subsequent command segmentHA_T1.sh https://secure-web.cisco.com/1Gwi-7iTclLyMc_ftX-27FkQ_lEVv_bPi_RnMqvKOoBX-mtc466lBReQuBYK2nT90kqsEJFh-61lTubnEuT-ivhUhu85qmvJFniCPzeyrNREUDtEezEt-blExFCoiPPs55hmp8maSfQ02RxECc7pY-4ud-4kPdGt33u_ZTX174QXYnfJnFdXryENiyyv-ac2a21tln00w-QJy2jnCjfLS4hkNvuR-tjgvUplqOg6Pz5PywNQtQ3n9kokR1FNdf48tLpO-Qpd-21x3lkOcjaGSiQ/https%3A%2F%2Fsgnldrp.live%2Fclick%3Fredirect%3Dhttp%253A%252F%252FsegmentHA_T1.sh%26dID%3D1614576832882%26linkName%3DsegmentHA_T1.sh bert, it gives me an error (even after modifying my .bashrc & .profile with export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/freesurfer/MCRv84/sys/os/glnxa64).
Also, I have tried sudo apt-get install libncurses5-dev. But that doesn't seem to resolve the issue.
P.s - The error is attached below for reference.
Thanks in advance.
On Wed, Feb 24, 2021 at 4:51 PM Ishi Tandon AIB, Jaipur <ishi.tandon@student.amity.edu mailto:ishi.tandon@student.amity.edu> wrote: Hello,
Thanks for those suggestions. I already seem to have modified my bashrc with the same command.
But I think running as root was a problem. But that's weird as earlier none of the Fs commands were executed without root.
But now that seems to work. However, I still need to check with segmentHa_T1 if that works well after recon-all.
Thanks for your help.
On Wed, Feb 24, 2021 at 6:54 AM Horsng Junn <hsjunn@gmail.com mailto:hsjunn@gmail.com> wrote: External Email - Use Caution
And you seem to be running FreeSurfer as root. Since that could complicate matters, could you run it as a normal user?
Best, Horsng
On Feb 24, 2021, at 9:36 AM, Horsng Junn <hsjunn@gmail.com mailto:hsjunn@gmail.com> wrote:
Hi Ishi,
I'm actually not a FreeSurfer developer and this question seems beyond me, but my googling leads to this page: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1TBSL0kryB96_RZZLIJVNWC7fxWomkLpTkc-kNGzwPbIbol... https://secure-web.cisco.com/1J96FRdW9b30grp2ZKVoOToURCtWoMNvRVujwywyg_8-dnzChY7mF4O26rtAy5IRwnW_AUTLc3NyneJNA50jjEVOXpbI4dZC473KwMJggVytdgBIRr71ekxd8YXDmrZITYqzNG0A84Oz0a0_j-f9chQHRFjVJfTuTpTAPNL4Wo-w6SWdOnsVA8JRnCaR8qo75dzxZNr7BeOYrzjdQM06h8MZJkqd1LV0hvaj__eT2EaJcoJ-8aqyXpOk3lldYcJCf/https%3A%2F%2Fwww.mathworks.com%2Fmatlabcentral%2Fanswers%2F459827-why-do-i-receive-a-glibcxx-not-found-error-on-my-redhat-or-centos-linux-machine
which seems to suggest that you add the following to your .bashrc, .profile or similar places and retry.
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/freesurfer/MCRv84/sys/os/glnxa64
Please try this and report your result. If this doesn't work, hopefully a FreeSurfer developer would chime in.
Best, Horsng
On Feb 23, 2021, at 8:19 PM, Ishi Tandon AIB, Jaipur <ishi.tandon@student.amity.edu mailto:ishi.tandon@student.amity.edu> wrote:
External Email - Use CautionHello,
I am sorry for posting up another thread. Had an issue with subscription so had to post again (will keep it in mind now).
I tried that out. And that worked well.
But there's another error that pops up after I run (attached in the image): - recon-all -all -s bert
I tried the following commands in order to update libstd. apt-get update apt-get install libstdc++6 But that didn't work.
I am not able to trace the exact error.
Thanks for the help.
On Tue, Feb 23, 2021 at 11:56 AM Horsng Junn <hsjunn@gmail.com mailto:hsjunn@gmail.com> wrote: External Email - Use Caution
Hi Ishi,
You apparently omitted an "n": it must be libncurses5-dev (please note the n after lib).
And please try to keep previous correspondences intact, as otherwise the devs must hunt the mail archive for the detail.
Best, Horsng
On Feb 23, 2021, at 3:10 PM, Ishi Tandon AIB, Jaipur <ishi.tandon@student.amity.edu mailto:ishi.tandon@student.amity.edu> wrote:
External Email - Use CautionHello experts,
In response to the previous email about matlab installation error while attempting to use hippocampal subfields.
I tried the following command as suggested by you :-
sudo apt-get install libcurses5-dev
But I get the following error :-
Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package libcurses5-dev
Also, I am using fs version 7.1.1. I installed freesurfer-linux-centos7_x86_64-7.1.1.tar.gz file.
Regards, Ishi Tandon B.Tech + M.Tech - Cognitive Neuroscience Amity University, Rajasthan Contact- +918239259846 Email - ishi.tandon99@gmail.com mailto:ishi.tandon99@gmail.com
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