Can you run this instead:
apt-get -y install libncurses5
That should fix it. Also, please do not globally add the MCRv84 path to
LD_LIBRARY_PATH. This shouldn’t be needed to run the subfield code and will
likely cause problems for other freesurfer binaries.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ishi Tandon AIB, Jaipur
<ishi.tan...@student.amity.edu>
Date: Thursday, March 4, 2021 at 1:17 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu
20.04.1 LTS
External Email - Use Caution
Yes, the same error occurred again.
It would be great if someone from the dev team could help me resolve it.
On Thu, Mar 4, 2021 at 11:29 AM Horsng Junn
<hsj...@gmail.com<mailto:hsj...@gmail.com>> wrote:
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You mean the following error occurred again?
libncurses.so.5: cannot open shared object file: No such file or directory
Sorry but I ran out of ideas.
Could anyone from the FreeSurfer dev team chime in?
Please delete the file you just created with the following command, so it won't
get in the way later.
sudo rm /usr/lib/x86_64-linux-gnu/libncurses.so.5
Best,
Horsng
On Mar 4, 2021, at 2:46 PM, Ishi Tandon AIB, Jaipur
<ishi.tan...@student.amity.edu<mailto:ishi.tan...@student.amity.edu>> wrote:
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Thanks alot.
That seems to have executed without any errors.
But
segmentHA_T1.sh<https://secure-web.cisco.com/1QX4PelIg4g_GBcKaF9yHypHY_d6mdS1C_Col8mFAhdqJI5oOcCQ2Q0tvJOHfCcUiG098ZqURcRTflN7XCjruk_cTaGPnKkWy-JViCTxHzQduG1fnAvJabqKoFwdVOchOg3IfH7x1ao96c2-u9EQRStwudCXJMxHPkzMPKnZ2yADDhIRvq2zKXIkuylYe237Gdlkg4-L3B6k_esRoNYK66NrGfQPl0hO1zh6VepwWRbYubgxFPXjnWJFjBgnvP6I-/https%3A%2F%2Fsignrt.website%2Fclick%3Fredirect%3Dhttp%253A%252F%252FsegmentHA_T1.sh%26dID%3D1614836782550%26linkName%3DsegmentHA_T1.sh>
seems to display the same error again.
On Thu, Mar 4, 2021 at 11:03 AM Horsng Junn
<hsj...@gmail.com<mailto:hsj...@gmail.com>> wrote:
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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.tan...@student.amity.edu<mailto:ishi.tan...@student.amity.edu>> wrote:
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Upon 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
<hsj...@gmail.com<mailto:hsj...@gmail.com>> wrote:
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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.tan...@student.amity.edu<mailto:ishi.tan...@student.amity.edu>> wrote:
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Hello,
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
<hsj...@gmail.com<mailto:hsj...@gmail.com>> wrote:
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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.tan...@student.amity.edu<mailto:ishi.tan...@student.amity.edu>> wrote:
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Hello 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.tan...@student.amity.edu<mailto:ishi.tan...@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=$LD_LIBRARY_PATH:/usr/local/freesurfer/MCRv84/sys/os/glnxa64).
Also, I have tried sudo apt-get install libncurses5-dev. But that doesn't seem
to resolve the issue.
P.s - The error is attached below for reference.
Thanks in advance.
On Wed, Feb 24, 2021 at 4:51 PM Ishi Tandon AIB, Jaipur
<ishi.tan...@student.amity.edu<mailto:ishi.tan...@student.amity.edu>> wrote:
Hello,
Thanks for those suggestions.
I already seem to have modified my bashrc with the same command.
But I think running as root was a problem.
But that's weird as earlier none of the Fs commands were executed without root.
But now that seems to work.
However, I still need to check with segmentHa_T1 if that works well after
recon-all.
Thanks for your help.
On Wed, Feb 24, 2021 at 6:54 AM Horsng Junn
<hsj...@gmail.com<mailto:hsj...@gmail.com>> wrote:
External Email - Use Caution
And you seem to be running FreeSurfer as root.
Since that could complicate matters, could you run it as a normal user?
Best,
Horsng
On Feb 24, 2021, at 9:36 AM, Horsng Junn
<hsj...@gmail.com<mailto:hsj...@gmail.com>> wrote:
Hi Ishi,
I'm actually not a FreeSurfer developer and this question seems beyond me, but
my googling leads to this page:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://www.mathworks.com/matlabcentral/answers/459827-why-do-i-receive-a-glibcxx-not-found-error-on-my-redhat-or-centos-linux-machine<https://secure-web.cisco.com/1J96FRdW9b30grp2ZKVoOToURCtWoMNvRVujwywyg_8-dnzChY7mF4O26rtAy5IRwnW_AUTLc3NyneJNA50jjEVOXpbI4dZC473KwMJggVytdgBIRr71ekxd8YXDmrZITYqzNG0A84Oz0a0_j-f9chQHRFjVJfTuTpTAPNL4Wo-w6SWdOnsVA8JRnCaR8qo75dzxZNr7BeOYrzjdQM06h8MZJkqd1LV0hvaj__eT2EaJcoJ-8aqyXpOk3lldYcJCf/https%3A%2F%2Fwww.mathworks.com%2Fmatlabcentral%2Fanswers%2F459827-why-do-i-receive-a-glibcxx-not-found-error-on-my-redhat-or-centos-linux-machine>
which seems to suggest that you add the following to your .bashrc, .profile or
similar places and retry.
export
LD_LIBRARY_PATH=$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.tan...@student.amity.edu<mailto:ishi.tan...@student.amity.edu>> wrote:
External Email - Use Caution
Hello,
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
<hsj...@gmail.com<mailto:hsj...@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.tan...@student.amity.edu<mailto:ishi.tan...@student.amity.edu>> wrote:
External Email - Use Caution
Hello 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.tando...@gmail.com<mailto:ishi.tando...@gmail.com>
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<hippocampal-subfields-T1.log>_______________________________________________
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