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Hello Melissa,
 If the GUI commands are running, then this is probably a configuration problem with your shell - what is the result of sourcing the fsl config file - e.g.

. $FSLDIR/etc/fslconf/fsl.sh

( please note the '. ' in the command above is important ).

Kind Regards
Matthew
Hello Matthew,

Unfortunately I dont have local administration rights, and the only platform that I have available is Windows, in which I'm trying to run the scripts through VNC viewer. The group melodic ICA analysis went fine (through the GUI), and I got all my results. But it is the dual regression script that is not working properly (on the terminal). Do you know of any other way of doing dual regression (another script or through any GUI). I was thinking I may have to change the FLSDIR to something else, because it is not reading the file that is in there. 

Any help would be greatly appreciated,

-Melissa H.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Matthew Webster <[log in to unmask]>
Sent: Tuesday, February 23, 2016 11:59 AM
To: [log in to unmask]
Subject: Re: [FSL] fslnvols error from dual regression
 
Hello Melissa,
  Unfortunately we have no experience with running the current version of FSL under cygwin, as it is no longer a supported platform. Our recommended solution for FSL on Windows is to use a virtual machine: please see


for the full instructions on how to download and configure a VM for your system.

Files like fslmaths, fsl_glm are binary data rather than scripts, and no attempt should be made to modify them with a text editor, as this could easily corrupt the files.

Hope this helps,
Kind Regards
Matthew

Hello Matthew,

I just use cigwin as the portal to get connected into VNC viewer and then run the scripts on the terminals. No, this FSL version was downloaded and adapted to this computer. Is there a way to reload these files, for instance: flsmaths, fslnvolvs, fsl_glm, fslmerge, fslsplit? When I tried to open one of these files through gedit, I get a message: 

"The file you opened has some invalid characters. If you continue editing this file you could corrupt this document. You can also choose another character encoding and try again."

Is there a way to edit this files the right way in order to try to run dual_regression again?

Thank you,

-Melissa H.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Matthew Webster <[log in to unmask]>
Sent: Tuesday, February 23, 2016 11:07 AM
To: [log in to unmask]
Subject: Re: [FSL] fslnvols error from dual regression
 
Hello Melissa,
 We haven't actively supported cygwin builds for some time - was this version of FSL built from source locally?
Kind Regards
Matthew

Good morning,

1) It is running on windows, within cigwin.
2) When I try to run fslmaths, it says: fslmaths: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory.

The same type of error message I was getting before, what could this be?

Thank you,

-Melissa H.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Matthew Webster <[log in to unmask]>
Sent: Tuesday, February 23, 2016 6:27 AM
To: [log in to unmask]
Subject: Re: [FSL] fslnvols error from dual regression
 
Hello,
   The script is failing at the first call to an FSL binary, can you confirm:

1) What platform is the VNC session running on ( the server, not the local machine )
2) On a terminal in the command line session, what happens if you run the FSL command "fslmaths" with no other command line arguements?

Kind Regards
Matthew

Good afternoon,

I'm running this through VNC viewer in a local machine. I believe there might be something else I need to put on the script, since it is running halfway, and then it just stops, I'm using FSL 5.0.

Thanks,

-Melissa H.


From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Mark Jenkinson <[log in to unmask]>
Sent: Monday, February 22, 2016 12:55 PM
To: [log in to unmask]
Subject: Re: [FSL] fslnvols error from dual regression
 
Hi,

What system are you running this on and how did you install FSL?
It looks like they are incompatible, based on the first error: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory.

All the best,
Mark

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of "Melissa H." <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Monday, 22 February 2016 17:25
To: "[log in to unmask]" <[log in to unmask]>
Subject: [FSL] fslnvols error from dual regression

Good afternoon,

I'm new to this program and I was trying to do group melodic ICA analysis. I got my melodic_IC output. However, when I tried to do dual regression, I got an error message:

creating common mask
doing the dual regressions
sorting maps and running randomize
/usr/share/fsl/5.0/bin/fslnvols: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory.
/usr/lib/fsl/5.0/dual_regression: 171: [: -lt: argument expected
wc: temp.dr.4/scripts+logs/drD: No such file or directory


I believe the error is in the fslnvolvs, since it seems to be stopping at that point. However, when I tried to open the files from scripts+logs, I also get error messages within the files:

drA: 2: Syntax error: EOF in backquote substitution

drB: /usr/share/fsl/5.0/bin/fslmerge: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory
/usr/share/fsl/5.0/bin/fslmaths: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory

Any help would be greatly appreciated!

Thanks,

Melissa H.