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Hello experts, 

With reference to my previous email, I am attaching the log file of segmentHA_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> wrote:
Hello experts, 

The recon-all command executed without any errors.

However, on following the subsequent  command segmentHA_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> 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> wrote:

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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> wrote:

Hi Ishi,

I'm actually not a FreeSurfer developer and this question seems beyond me, but my googling leads to this page:

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> wrote:

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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 <hsjunn@gmail.com> wrote:

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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> wrote:

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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

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