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]
|