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Hi James,Thanks for the additional information. I'm still not sure what caused the error, so let me know if it happens for you again.Cheers,PaulOn 12 September 2018 at 21:38, James Gullickson <[log in to unmask]> wrote:Here is the answer from our IT dept:The compute cluster as well as the standalone compute hosts are running Ubuntu 14.04. The standalone version of FSLEyes was installed and the fsl 5.0.11 module sets the path to the installation directory.
On Wed, Sep 12, 2018 at 1:13 PM, James Gullickson <[log in to unmask]> wrote:Paul,I spoke with our IT department and they updated FSLeyes to version 0.25.0. This seems to have fixed the problem, as I am now able to view the files without getting the error. I will go ahead an upload one of the offending files anyway in case you want to take a look.As far as server OS version and how FSLeyes has been installed, I'm not sure how to check that, so I will email our IT and get back to you. Practically, I access FSLeyes via:ssh (servername)module load fsl/5.0.11fsleyesThe path to the installation ("which fsleyes") reads:/pkg/software_depot/app/fsleyes/ubuntu_14.04/FSLeyes/fsleyes Thanks,JamesOn Thu, Sep 6, 2018 at 4:59 AM, paul mccarthy <[log in to unmask]> wrote:Hi James,What operating system is your server running, and how has FSLeyes been installed - e.g. from a standalone version, or into a Python environment?Would you mind sharing the offending file? You can upload it at:
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=620487CFE237E0 D565
Cheers,
PaulOn 5 September 2018 at 20:01, James Gullickson <[log in to unmask]> wrote:It has been happening consistently when I use my institution's set-up of fsl 5.0.11 (accessed via "module load fsl/5.0.11")Just checked the fsleyes version. It's 0.22.4 with the 5.0.11 set-up, and 0.18.2 with the 5.0.9 set-up. I have asked my system admin to update to the latest version.Below is the text outputted to the terminal when I attempt to load one of these images into fsleyes. Is this at all illuminating?fsleyes output.feat/ICA_AROMA/denoised_func_data_nonaggr.nii.gz 13:08:57: Debug: Adding duplicate image handler for 'Windows bitmap file'/pkg/software_depot/app/fsl/5.0.11/ubuntu_14.04/bin/FSLeyes/ fsl/data/image.py:1455: DeprecationWarning: guessed_image_type deprecated.2.1 * deprecated from version: 4.0/pkg/software_depot/app/fsl/5.0.11/ubuntu_14.04/bin/FSLeyes/ fsl/data/image.py:1459: DeprecationWarning: SafeIndexedGzilFile is deprecated - use IndexedGzipFile instead (fsleyes:30227): Gdk-WARNING **: /build/gtk+2.0-KsZSEA/gtk+2.0-2.24.23/gdk/x11/gdkdrawable-x1 1.c:952 drawable is not a pixmap or window Segmentation faultThanks,JamesOn Wed, Sep 5, 2018 at 12:54 PM, paul mccarthy <[log in to unmask]> wrote:Hi James,That is a strange error. Does it happen every time you try to view the image, or only sporadically?What version of FSLeyes are you using (fsleyes -V)? Have you tried the latest version (get it from https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes )?Cheers,PaulOn 5 September 2018 at 18:00, James Gullickson <[log in to unmask]> wrote:Dear FSL experts,I am working on a preprocessing script for resting state fMRI and am running into an issue when trying to view certain output files from this pipeline with FSLeyes in fsl version 5.0.11. The error I get is:An error occurred loading the image/path/to/file.nii.gzDetails: I/O operation on uninitialized objectThe first file that triggers this error is filtered_func_data.nii.gz from the feat output.I am able to view the files in fsleyes or fslview when using fsl version 5.0.9, however.Any idea what's going on? Any input is appreciated.The pipeline is attached for reference.Thanks,James
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