Hello Melissa,
			  Can you let me know the full command line call you used, also can you confirm that in the directory you are running dual_regression in, groupmelodic.ica/melodic_IC.nii.gz exists?

Kind Regards
Matthew
> Hello,
> 
> I finally got all the permissions to work on fsl on this computer. However, I'm now getting a new error message after running dual regression:
> 
> DrC.e: Could not open matrix file groupmelodic.ica/melodic_IC
> ols_dof: Error in determining the trace, resorting to basic calculation
> ols_dof: Error in determining the trace, resorting to basic calculation
> Cannot open volume temp.dr.xfm/dr_stage2_subject00000 for reading!
> 
> I got dr_stage1 and dr_stage2 files but not 3. Also, when setting up my GLM con and mat, I didn't get any "filest.txt" so I created it myself using the filtered_func_data from the "reg_standard" folder. I also tried to flirtered the filtered func data to see if I get any diff output but still the same error..
> 
> What could I be doing wrong?
> 
> Thank you in advance,
> 
> -Melissa H.
> 
> ________________________________________
> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Niels Bergsland <[log in to unmask]>
> Sent: Wednesday, February 24, 2016 3:21 PM
> To: [log in to unmask]
> Subject: Re: [FSL] fslnvols error from dual regression
> 
> Hi -
> I just meant that it was normal that you didn't get any output from
> running ". $FSLDIR/etc/fslconf/fsl.sh"  That file should just set up
> your environment for using FSL.
> 
> After you run that command, what happens if you try running in that terminal:
> 
> /usr/share/fsl/5.0/bin/fslnvols
> 
> On Wed, Feb 24, 2016 at 8:34 PM, Hidalgo, Melissa <[log in to unmask]> wrote:
>> Hello Niels,
>> 
>> What does that mean? Is there a way that I can change the fsl.sh? or do you think I should re-install fsl, would that change anything?
>> 
>> Thank you,
>> 
>> -Melissa H.
>> ________________________________________
>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Niels Bergsland <[log in to unmask]>
>> Sent: Wednesday, February 24, 2016 1:05 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] fslnvols error from dual regression
>> 
>> Hi Melissa,
>> The first one is correct - it doesn't actually produce any output - it
>> just sets up some shell variables.
>> 
>> The second gives you that error because it is looking for
>> "usr/share/fsl/5.0/etc/fslconf/fsl.sh" under your current working
>> directory.
>> 
>> Best,
>> Niels
>> 
>> On Wed, Feb 24, 2016 at 6:59 PM, Hidalgo, Melissa <[log in to unmask]> wrote:
>>> Hello Niels,
>>> 
>>> 
>>> If I put a space it doesnt do anything, the next line that appears is
>>> (blank): @detective:~$
>>> 
>>> But, if I dont put the space then I get:
>>> 
>>> bash: ./usr/share/fsl/5.0/etc/fslconf/fsl.sh: No such file or directory
>>> 
>>> 
>>> -Melissa H.
>>> 
>>> 
>>> ________________________________
>>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Niels
>>> Bergsland <[log in to unmask]>
>>> Sent: Wednesday, February 24, 2016 12:53 PM
>>> 
>>> To: [log in to unmask]
>>> Subject: Re: [FSL] fslnvols error from dual regression
>>> 
>>> Hi - Your command is missing a space.
>>> 
>>> It should be:
>>> 
>>> . $FSLDIR/etc/fslconf/fsl.sh
>>> 
>>> not
>>> 
>>> .$FSLDIR/etc/fslconf/fsl.sh
>>> 
>>> Best,
>>> Niels
>>> 
>>> On Wed, Feb 24, 2016 at 6:49 PM, Hidalgo, Melissa <[log in to unmask]> wrote:
>>>> 
>>>> Hello Matthew,
>>>> 
>>>> 
>>>> So I'm putting this:
>>>> 
>>>> .$FSLDIR/etc/fslconf/fsl.sh
>>>> 
>>>> 
>>>> and I'm getting this:
>>>> 
>>>> bash: ./usr/share/fsl/5.0/etc/fslconf/fsl.sh: No such file or directory
>>>> 
>>>> 
>>>> Even though the fsl.sh file is there. Is there a way to change the script
>>>> of the fsl.sh file so that it reads the other fsl binary files?
>>>> 
>>>> 
>>>> Thank you so much,
>>>> 
>>>> 
>>>> -Melissa H.
>>>> 
>>>> 
>>>> ________________________________
>>>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of
>>>> Matthew Webster <[log in to unmask]>
>>>> Sent: Wednesday, February 24, 2016 10:54 AM
>>>> 
>>>> To: [log in to unmask]
>>>> Subject: Re: [FSL] fslnvols error from dual regression
>>>> 
>>>> 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
>>>> 
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__fsl.fmrib.ox.ac.uk_fsl_fslwiki_FslInstallation_Windows&d=CwIBaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=eUjRRWNzkwKGsO9WQsZhZQ&m=OerBNu7fh-ZXtuuSh6bzx2pBpNkT8EZIv1F5wuuOU5w&s=KCZMbPnarD6DoJob0ZVqPayJpg3eCPMDFEDAAjBO3I4&e=
>>>> 
>>>> 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.
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> Niels Bergsland
>>> Integration Director
>>> Buffalo Neuroimaging Analysis Center
>>> 100 High St. Buffalo NY 14203
>>> [log in to unmask]
>> 
>> 
>> 
>> --
>> Niels Bergsland
>> Integration Director
>> Buffalo Neuroimaging Analysis Center
>> 100 High St. Buffalo NY 14203
>> [log in to unmask]
> 
> 
> 
> --
> Niels Bergsland
> Integration Director
> Buffalo Neuroimaging Analysis Center
> 100 High St. Buffalo NY 14203
> [log in to unmask]