Can't see GUI in Ubuntu

[egarza]

I have Linux Ubuntu 16.04 LTS Xenial. It seems I cannot get the GUI even with the instructions given. Any help is appreciated.

Here is the code and the error:

sudo docker run -i --rm --privileged -e DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v /tmp:/scratch -v /media/egarza/INP_MRI_Backup/projects/INP/addimex_tms/data/mri/nifti:/bids_dataset -v /media/egarza/INP_MRI_Backup/projects/INP/addimex_tms/data/mri/outputs:/outputs bids/cpac /bids_dataset /outputs GUI No protocol specified Namespace(analysis_level='GUI', aws_input_creds=None, aws_output_creds=None, bids_dir='/bids_dataset', data_config_file=None, mem_gb=None, mem_mb=None, n_cpus='1', output_dir='/outputs', participant_label=None, participant_ndx=None, pipeline_file='/cpac_resources/default_pipeline.yaml', save_working_dir=False) Starting CPAC GUI Unable to access the X Display, is $DISPLAY set properly?

[ccraddock]

We will look at this. Sorry for the delay.

…

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On Jul 29, 2017, at 1:15 PM, Eduardo Garza-Villarreal ***@***.***> wrote: I have Linux Ubuntu 16.04 LTS Xenial. It seems I cannot get the GUI even with the instructions given. Any help is appreciated. Here is the code and the error: sudo docker run -i --rm --privileged -e DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v /tmp:/scratch -v /media/egarza/INP_MRI_Backup/projects/INP/addimex_tms/data/mri/nifti:/bids_dataset -v /media/egarza/INP_MRI_Backup/projects/INP/addimex_tms/data/mri/outputs:/outputs bids/cpac /bids_dataset /outputs GUI No protocol specified Namespace(analysis_level='GUI', aws_input_creds=None, aws_output_creds=None, bids_dir='/bids_dataset', data_config_file=None, mem_gb=None, mem_mb=None, n_cpus='1', output_dir='/outputs', participant_label=None, participant_ndx=None, pipeline_file='/cpac_resources/default_pipeline.yaml', save_working_dir=False) Starting CPAC GUI Unable to access the X Display, is $DISPLAY set properly? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[egarza]

No problem, sir. I tried several fixes such as [this] (http://fabiorehm.com/blog/2014/09/11/running-gui-apps-with-docker/), but no luck.

Thanks

Ed

[ccraddock]

Are you willing to try installing singilarity? It should just work

…

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On Aug 1, 2017, at 11:31 AM, Eduardo Garza-Villarreal ***@***.***> wrote: No problem, sir. I tried several fixes such as this [http://fabiorehm.com/blog/2014/09/11/running-gui-apps-with-docker/], but no luck. Thanks Ed — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[egarza]

I did that already, then tried to import the docker2singularity cpac with no luck. I get an error. Let me paste that error.
Is there a way to setup cpac from singularity instead of using the converter?

[egarza]

sudo docker run --privileged -ti --rm -v /var/run/docker.sock:/var/run/docke
r.sock -v /home/egarza/MRI/apps/singularity_images:/output singularityware/docker2singularity bids/cpac
Size: 5533 MB for the singularity container
(1/9) Creating an empty image...
Creating a sparse image with a maximum size of 5533MiB...
Using given image size of 5533
Formatting image (/sbin/mkfs.ext3)
Done. Image can be found at: /tmp/bids_cpac-2017-03-29-71120146c4f4.img
(2/9) Importing filesystem...
(3/9) Bootstrapping...
(4/9) Adding run script...
(5/9) Setting ENV variables...
Singularity: sexec (U=0,P=146)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh
(6/9) Adding mount points...
Singularity: sexec (U=0,P=152)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh
(7/9) Fixing permissions...
Singularity: sexec (U=0,P=158)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh
We're running on BusyBox/Buildroot
Singularity: sexec (U=0,P=201)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh
find: `/proc/2/task/2/fd/11': No such file or directory
find: `/proc/2/task/2/fd/11': No such file or directory
find: `/proc/2/task/2/fdinfo/11': No such file or directory
find: `/proc/2/task/2/fdinfo/11': No such file or directory
find: `/proc/2/fd/11': No such file or directory
find: `/proc/2/fd/11': No such file or directory
find: `/proc/2/fdinfo/11': No such file or directory
find: `/proc/2/fdinfo/11': No such file or directory

[ccraddock]

I have a singularity image you can download. I will send info later today.

…

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On Aug 1, 2017, at 11:42 AM, Eduardo Garza-Villarreal ***@***.***> wrote: sudo docker run --privileged -ti --rm -v /var/run/docker.sock:/var/run/docke r.sock -v /home/egarza/MRI/apps/singularity_images:/output singularityware/docker2singularity bids/cpac Size: 5533 MB for the singularity container (1/9) Creating an empty image... Creating a sparse image with a maximum size of 5533MiB... Using given image size of 5533 Formatting image (/sbin/mkfs.ext3) Done. Image can be found at: /tmp/bids_cpac-2017-03-29-71120146c4f4.img (2/9) Importing filesystem... (3/9) Bootstrapping... (4/9) Adding run script... (5/9) Setting ENV variables... Singularity: sexec (U=0,P=146)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh (6/9) Adding mount points... Singularity: sexec (U=0,P=152)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh (7/9) Fixing permissions... Singularity: sexec (U=0,P=158)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh We're running on BusyBox/Buildroot Singularity: sexec (U=0,P=201)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh find:/proc/2/task/2/fd/11': No such file or directory find: /proc/2/task/2/fd/11': No such file or directory find:/proc/2/task/2/fdinfo/11': No such file or directory find: /proc/2/task/2/fdinfo/11': No such file or directory find:/proc/2/fd/11': No such file or directory find: /proc/2/fd/11': No such file or directory find:/proc/2/fdinfo/11': No such file or directory find: /proc/2/fdinfo/11': No such file or directory — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[egarza]

Cool, thanks.

[egarza]

As a follow-up, my student just installed bids/cpac in his Macbook Pro OSX El Capitan. We did all the instructions to get the Display, and we get the same error with Display.

[egarza]

Tried with singularity and GUI worked like a charm.

Now, I tried to make and save a subjects list and gave me the same error as with the full CPAC:

singularity run -B /home/egarza:/mnt -B /mnt:/scratch -B /media/egarza/INP_MRI_Backup/projects/INP/addimex_tms/data/mri/bids:/bids_dataset -B /media/egarza/INP_MRI_Backup/projects/INP/addimex_tms/data/mri/outputs:/output /home/egarza/MRI/apps/singularity_images/bids_cpac-2017-03-29-a12af7f5d881.img /bids_dataset /output GUI 
Namespace(analysis_level='GUI', aws_input_creds=None, aws_output_creds=None, bids_dir='/bids_dataset', data_config_file=None, mem_gb=None, mem_mb=None, n_cpus='1', output_dir='/output', participant_label=None, participant_ndx=None, pipeline_file='/cpac_resources/default_pipeline.yaml', save_working_dir=False)
Starting CPAC GUI
Gtk-Message: Failed to load module "gail"
Gtk-Message: Failed to load module "atk-bridge"
Gtk-Message: Failed to load module "unity-gtk-module"
Gtk-Message: Failed to load module "canberra-gtk-module"

(run.py:30602): Gtk-WARNING **: Unable to find default local file monitor type

(run.py:30602): Gtk-WARNING **: Unable to find default local file monitor type
saving /media/egarza/INP_MRI_Backup/projects/INP/addimex_tms/data/mri/data_config_addimex_tms.yaml
Gathering anatomical files...
2017-08-01 13:39:46,657 : Found 19 files!
170801-13:39:46,657 sublist_builder INFO:
	 Found 19 files!
Gathering functional files...
2017-08-01 13:39:46,658 : Found 17 files!
170801-13:39:46,658 sublist_builder INFO:
	 Found 17 files!
2017-08-01 13:39:46,658 : Filtering anatomical files...
170801-13:39:46,658 sublist_builder INFO:
	 Filtering anatomical files...
2017-08-01 13:39:46,658 : Not filtering out any potential sites...
170801-13:39:46,658 sublist_builder INFO:
	 Not filtering out any potential sites...
2017-08-01 13:39:46,658 : Filtered down to 19 files
170801-13:39:46,658 sublist_builder INFO:
	 Filtered down to 19 files
Filtered down to 19 anatomical files
2017-08-01 13:39:46,658 : Not filtering out any potential sites...
170801-13:39:46,658 sublist_builder INFO:
	 Not filtering out any potential sites...
2017-08-01 13:39:46,658 : Filtered down to 17 files
170801-13:39:46,658 sublist_builder INFO:
	 Filtered down to 17 files

(run.py:30602): Gtk-WARNING **: Unable to find default local file monitor type
Error importing CPAC
cannot import name fsopendir

Is there a conflict between cpacs?

Thanks

Ed

[egarza]

Still can't save the data nor pipeline files using the GUI with singularity. I opted for editing the regular pipeline, but it would greatly help our work if we could do it from the GUI at some point, specially for teaching reasons.

Thanks
Ed

[czarrar]

I am having the same issue with an ubuntu machine (14.04.5 LTS). The issue being: "Unable to access the X Display, is $DISPLAY set properly?" Has there been any resolution to using docker?

[ccraddock]

i have been able to use it following these instructions: https://github.com/bids-apps/cpac#running-docker-container-on-linux make sure that you are correctly passing the DISPLAY environment variable into the container

…

On Fri, Jun 29, 2018 at 1:09 PM Zarrar Shehzad ***@***.***> wrote: I am having the same issue with an ubuntu machine (14.04.5 LTS). The issue being: "Unable to access the X Display, is $DISPLAY set properly?" Has there been any resolution to using docker? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABpTWEhBvh95yued27Dx43z91eVLh7kyks5uBm1TgaJpZM4OnaPh> .

-- Associate Professor of Diagnostic Medicine, Dell Medical School at the University of Texas at Austin Director, Computational NeuroImaging Lab <http://computational-neuroimaging-lab.org/> Founding Chair, Organization for Human Brain Mapping Open Science Special Interest Group Co-Founder, The Neuro Bureau <http://neurobureau.org/> Impact Story <https://impactstory.org/CameronCraddock> Google Scholar Citations <http://scholar.google.com/citations?user=lZ9hwSsAAAAJ&hl=en> GitHub <https://github.com/ccraddock> SlideShare <http://www.slideshare.net/CameronCraddock> Check out my recent blog Open Science Resources for Contributing to Brain Imaging Research <http://blogs.biomedcentral.com/gigablog/2016/03/15/open-science-resources-contributing-brain-imaging-research-guest-blog-cameron-craddock/> Share that Brain @ the International Neuroimaging Datasharing Initiative <http://fcon_1000.projects.nitrc.org/>! The GigaScience Brainhack Thematic Series <http://brainhack.org/brainhack-thematic-series-call-for-papers/> is open for your submission. Submit a paper to the Neuroimage Special Issue on Brain Segmentation and Parcellation <http://www.journals.elsevier.com/neuroimage/call-for-papers/brain-segmentation-and-parcellation/> ! The Preprocessed Connectomes Project <http://preprocessed-connectomes-project.org/> is now sharing preprocessed versions of the ABIDE and ADHD200 neuroimaging datasets. Join me at upcoming Brainhack <http://brainhack.org/> Events: 2017.03.02 - 2016.03.05 Brainhack Global <http://events.brainhack.org/global2017> Remember to submit your Brainhack Project Report to the 2016 Brainhack Proceedings <http://brainhack.org/proceedings>

[ccraddock]

or try singularity, it just works On Fri, Jun 29, 2018 at 1:10 PM Cameron Craddock <cameron.craddock@gmail.com> wrote:

…

i have been able to use it following these instructions: https://github.com/bids-apps/cpac#running-docker-container-on-linux make sure that you are correctly passing the DISPLAY environment variable into the container On Fri, Jun 29, 2018 at 1:09 PM Zarrar Shehzad ***@***.***> wrote: > I am having the same issue with an ubuntu machine (14.04.5 LTS). The > issue being: "Unable to access the X Display, is $DISPLAY set properly?" > Has there been any resolution to using docker? > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#11 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/ABpTWEhBvh95yued27Dx43z91eVLh7kyks5uBm1TgaJpZM4OnaPh> > . > -- Associate Professor of Diagnostic Medicine, Dell Medical School at the University of Texas at Austin Director, Computational NeuroImaging Lab <http://computational-neuroimaging-lab.org/> Founding Chair, Organization for Human Brain Mapping Open Science Special Interest Group Co-Founder, The Neuro Bureau <http://neurobureau.org/> Impact Story <https://impactstory.org/CameronCraddock> Google Scholar Citations <http://scholar.google.com/citations?user=lZ9hwSsAAAAJ&hl=en> GitHub <https://github.com/ccraddock> SlideShare <http://www.slideshare.net/CameronCraddock> Check out my recent blog Open Science Resources for Contributing to Brain Imaging Research <http://blogs.biomedcentral.com/gigablog/2016/03/15/open-science-resources-contributing-brain-imaging-research-guest-blog-cameron-craddock/> Share that Brain @ the International Neuroimaging Datasharing Initiative <http://fcon_1000.projects.nitrc.org/>! The GigaScience Brainhack Thematic Series <http://brainhack.org/brainhack-thematic-series-call-for-papers/> is open for your submission. Submit a paper to the Neuroimage Special Issue on Brain Segmentation and Parcellation <http://www.journals.elsevier.com/neuroimage/call-for-papers/brain-segmentation-and-parcellation/> ! The Preprocessed Connectomes Project <http://preprocessed-connectomes-project.org/> is now sharing preprocessed versions of the ABIDE and ADHD200 neuroimaging datasets. Join me at upcoming Brainhack <http://brainhack.org/> Events: 2017.03.02 - 2016.03.05 Brainhack Global <http://events.brainhack.org/global2017> Remember to submit your Brainhack Project Report to the 2016 Brainhack Proceedings <http://brainhack.org/proceedings>

-- Associate Professor of Diagnostic Medicine, Dell Medical School at the University of Texas at Austin Director, Computational NeuroImaging Lab <http://computational-neuroimaging-lab.org/> Founding Chair, Organization for Human Brain Mapping Open Science Special Interest Group Co-Founder, The Neuro Bureau <http://neurobureau.org/> Impact Story <https://impactstory.org/CameronCraddock> Google Scholar Citations <http://scholar.google.com/citations?user=lZ9hwSsAAAAJ&hl=en> GitHub <https://github.com/ccraddock> SlideShare <http://www.slideshare.net/CameronCraddock> Check out my recent blog Open Science Resources for Contributing to Brain Imaging Research <http://blogs.biomedcentral.com/gigablog/2016/03/15/open-science-resources-contributing-brain-imaging-research-guest-blog-cameron-craddock/> Share that Brain @ the International Neuroimaging Datasharing Initiative <http://fcon_1000.projects.nitrc.org/>! The GigaScience Brainhack Thematic Series <http://brainhack.org/brainhack-thematic-series-call-for-papers/> is open for your submission. Submit a paper to the Neuroimage Special Issue on Brain Segmentation and Parcellation <http://www.journals.elsevier.com/neuroimage/call-for-papers/brain-segmentation-and-parcellation/> ! The Preprocessed Connectomes Project <http://preprocessed-connectomes-project.org/> is now sharing preprocessed versions of the ABIDE and ADHD200 neuroimaging datasets. Join me at upcoming Brainhack <http://brainhack.org/> Events: 2017.03.02 - 2016.03.05 Brainhack Global <http://events.brainhack.org/global2017> Remember to submit your Brainhack Project Report to the 2016 Brainhack Proceedings <http://brainhack.org/proceedings>

[egarza]

Hi Cam,

We still get the same error with Docker. In different computers with Ubuntu.
Singularity works with the GUI but we are still unable to save the YML file.

[ccraddock]

OK, i will look into this again.

…

On Fri, Jun 29, 2018 at 1:56 PM Eduardo Garza-Villarreal < ***@***.***> wrote: Hi Cam, We still get the same error with Docker. In different computers with Ubuntu. Singularity works with the GUI but we are still unable to save the YML file. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABpTWHH4EfUB1LdgbEqDTOMH9aV39OS-ks5uBnhrgaJpZM4OnaPh> .

-- Associate Professor of Diagnostic Medicine, Dell Medical School at the University of Texas at Austin Director, Computational NeuroImaging Lab <http://computational-neuroimaging-lab.org/> Founding Chair, Organization for Human Brain Mapping Open Science Special Interest Group Co-Founder, The Neuro Bureau <http://neurobureau.org/> Impact Story <https://impactstory.org/CameronCraddock> Google Scholar Citations <http://scholar.google.com/citations?user=lZ9hwSsAAAAJ&hl=en> GitHub <https://github.com/ccraddock> SlideShare <http://www.slideshare.net/CameronCraddock> Check out my recent blog Open Science Resources for Contributing to Brain Imaging Research <http://blogs.biomedcentral.com/gigablog/2016/03/15/open-science-resources-contributing-brain-imaging-research-guest-blog-cameron-craddock/> Share that Brain @ the International Neuroimaging Datasharing Initiative <http://fcon_1000.projects.nitrc.org/>! The GigaScience Brainhack Thematic Series <http://brainhack.org/brainhack-thematic-series-call-for-papers/> is open for your submission. Submit a paper to the Neuroimage Special Issue on Brain Segmentation and Parcellation <http://www.journals.elsevier.com/neuroimage/call-for-papers/brain-segmentation-and-parcellation/> ! The Preprocessed Connectomes Project <http://preprocessed-connectomes-project.org/> is now sharing preprocessed versions of the ABIDE and ADHD200 neuroimaging datasets. Join me at upcoming Brainhack <http://brainhack.org/> Events: 2017.03.02 - 2016.03.05 Brainhack Global <http://events.brainhack.org/global2017> Remember to submit your Brainhack Project Report to the 2016 Brainhack Proceedings <http://brainhack.org/proceedings>