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bids-apps / CPAC

BIDS Application for the Configurable Pipeline for the Analysis of Connectomes (C-PAC)
Apache License 2.0
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Can't see GUI in Ubuntu #11

Open egarza opened 7 years ago

egarza commented 7 years ago

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 commented 7 years ago

We will look at this. Sorry for the delay.

Sent from my iPhone

On Jul 29, 2017, at 1:15 PM, Eduardo Garza-Villarreal notifications@github.com 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?

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egarza commented 7 years ago

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 commented 7 years ago

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 notifications@github.com 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

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egarza commented 7 years ago

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 commented 7 years ago 
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 commented 7 years ago

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 notifications@github.com 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

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egarza commented 7 years ago

Cool, thanks.

egarza commented 7 years ago

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 commented 7 years ago

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 commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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 notifications@github.com 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 https://github.com/BIDS-Apps/CPAC/issues/11#issuecomment-401431772, 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.

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ccraddock commented 6 years ago

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 notifications@github.com 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 https://github.com/BIDS-Apps/CPAC/issues/11#issuecomment-401431772, 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

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egarza commented 6 years ago

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 commented 6 years ago

OK, i will look into this again.

On Fri, Jun 29, 2018 at 1:56 PM Eduardo Garza-Villarreal < notifications@github.com> 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 https://github.com/BIDS-Apps/CPAC/issues/11#issuecomment-401443987, 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

czarrar commented 6 years ago

I have the reverse problem. I can save the YAML file with singularity but when I try to run preprocessing, it doesn't do anything. Well it shows one line (below) but then nothing is run.

strategy_entries: [['_compcor_ncomponents_5_selector_pc10.linear0.wm0.global0.motion1.quadratic0.gm0.compcor1.csf0', '_target_angle_deg_90', '_threshold_0.2']]

But if I run with participant mode instead of GUI using the yaml files saved by the GUI, then it runs for me with singularity.

ccraddock commented 6 years ago

Which singularity container are you using?

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On Jun 30, 2018, at 5:55 PM, Zarrar Shehzad notifications@github.com wrote:

I have the reverse problem. I can save the YAML file with singularity but when I try to run preprocessing, it doesn't do anything. Well it shows one line (below) but then nothing is run.

strategy_entries: [['_compcor_ncomponents_5_selector_pc10.linear0.wm0.global0.motion1.quadratic0.gm0.compcor1.csf0', '_target_angle_deg_90', '_threshold_0.2']]

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czarrar commented 6 years ago

The one I made by converting the CPAC docker to singularity.

ccraddock commented 6 years ago

Ok. What version of the docket container

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On Jun 30, 2018, at 9:40 PM, Zarrar Shehzad notifications@github.com wrote:

The one I made by converting the CPAC docker to singularity.

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ccraddock commented 6 years ago

I was able to get the GUI to work using x11docker (https://github.com/mviereck/x11docker). Would you mind trying that? This sample worked for me: x11docker --bids/cpac /tmp /tmp GUI

egarza commented 6 years ago

I am able to run the GUI that way, I include the --homedir flag and it works.

I can save the Subject file, but when I try to Generate the Subject YAML it tells me this:

screenshot from 2018-07-02 14-45-40

ccraddock commented 6 years ago

I will look into this further. In the meantime, can you generate your data config file using the 'test_config' flag to the CPAC app? Also, you appear to be using an older version of CPAC (the logo is different), perhaps you could try with a newer version?

czarrar commented 6 years ago

Everything works for me now in singularity. There was a path issue for the inputs that wasn't being displayed.

ccraddock commented 6 years ago

@czarrar would you please elaborate so that we can fix the error reporting in future versions?

czarrar commented 6 years ago

When running in the 'participant' instead of 'GUI' option, I saw that I had improper BIDS paths that was causing an issue. In the 'GUI' setting, when I ran the analysis, it didn't show this error or any of the output that comes with CPAC. However, when I fixed the path issue, then going through the 'GUI' ran fine. Hope this helps.

egarza commented 6 years ago

I downloaded the latest bids/cpac. Now it does not give me the error, but it also does not Generate the Data Config file. And still, the CPAC looks as if it crashed but it is still responsive. Very strange. I will use the test_config and see if I can save the pipeline. Thanks

egarza commented 6 years ago

Made Singularity GUI work using the instructions. Now I did not have a problem converting the docker image to singularity and it all opened fine. I do have a problem, but I made it another Issue. It may seem this new issue is similar to the Docker issue with x11docker as it has to do more with the Path Search.