slicer DMRI Extensions

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slicer DMRI Extensions

Jeff Stevenson-2
Hi slicer folks, been following the latest module releases of DMRI and UKFT . i tried to download the same dev version today 4.7.0-2017-02-18 r25712.
on my mac the module install fine. on my 14.04 linux workstation i get a dependency error

“the extension Eigen could not be found. the extension
may not work properly.”

tractography display seems not to be installed when this happens, so DMRI/UKFT build on linux still has some issues.

cheers jeff

btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.
 
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Re: slicer DMRI Extensions

inorton
Hi Jeff,

Thanks for the feedback!

Unfortunately, on Linux it looks like SlicerDMRI, UKF, and a number of other modules have empty package download files in the current nightly (tried SlicerRT, TCIABrowser, DSCMRIAnalysis, SlicerPathology, IntensitySegmenter). There are messages in the Slicer error log about empty archives, but regrettably the extension manager doesn't currently provide any prominent error message about this type of install failure.


btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

Not sure about this one -- I believe each version should have its own config sub-folder, and at least on Mac any downloaded extensions are stored inside the version-specific app bundle.

The Eigen notice is present on all platforms but should not affect functionality of either the main DMRI modules or UKF, when they are otherwise installed correctly. I'll see if I can find a way to fix the message.

Best,
Isaiah


On Tue, Feb 21, 2017 at 2:03 PM, Jeff Stevenson <[hidden email]> wrote:
Hi slicer folks, been following the latest module releases of DMRI and UKFT . i tried to download the same dev version today 4.7.0-2017-02-18 r25712.
on my mac the module install fine. on my 14.04 linux workstation i get a dependency error

“the extension Eigen could not be found. the extension
may not work properly.”

tractography display seems not to be installed when this happens, so DMRI/UKFT build on linux still has some issues.

cheers jeff

btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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Re: slicer DMRI Extensions

Jeff Stevenson-2
In reply to this post by Jeff Stevenson-2
Hi isaiah, fyi when the eigen notice pops up the module for fiber tract display is missing. Not sure if that is a coincidence, but without the display module its not usable. Is there a manual workaround?

I tried the latest release and was unable to download any of the diffusion tool kit. Gave script error dialogue. No love.
Jeff


From: Isaiah Norton
Date: Wednesday, March 1, 2017 at 9:28 AM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thanks for the feedback!

Unfortunately, on Linux it looks like SlicerDMRI, UKF, and a number of other modules have empty package download files in the current nightly (tried SlicerRT, TCIABrowser, DSCMRIAnalysis, SlicerPathology, IntensitySegmenter). There are messages in the Slicer error log about empty archives, but regrettably the extension manager doesn't currently provide any prominent error message about this type of install failure.


btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

Not sure about this one -- I believe each version should have its own config sub-folder, and at least on Mac any downloaded extensions are stored inside the version-specific app bundle.

The Eigen notice is present on all platforms but should not affect functionality of either the main DMRI modules or UKF, when they are otherwise installed correctly. I'll see if I can find a way to fix the message.

Best,
Isaiah


On Tue, Feb 21, 2017 at 2:03 PM, Jeff Stevenson <[hidden email]> wrote:
Hi slicer folks, been following the latest module releases of DMRI and UKFT . i tried to download the same dev version today 4.7.0-2017-02-18 r25712.
on my mac the module install fine. on my 14.04 linux workstation i get a dependency error

“the extension Eigen could not be found. the extension
may not work properly.”

tractography display seems not to be installed when this happens, so DMRI/UKFT build on linux still has some issues.

cheers jeff

btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: slicer DMRI Extensions

inorton
In reply to this post by Jeff Stevenson-2
Hi Jeff,

Thank you for your patience, I apologize for these problems. Going forward we will be creating "snapshot" packages with SlicerDMRI pre-installed, on a regular basis (~monthly).

We will link to these snapshots as the recommended installation method on our website. The extension will still be available in the nightly too, but in light of various extension download issues [1], we are going to experiment with snapshots as a better way to create a smooth installation process.

To that end: I have created an initial snapshot against the Slicer Linux nightly from 3/12, available to download here:


I tested this on an Ubuntu 14.04 virtualbox VM, and the seeding/display features work as expected (attached screenshot [2]).  I will script up the process and create similar packages for Mac and Windows shortly, and upload to the same location. I hope that this works correctly, but please let me know if not.

Regarding 4.6.2 on Linux, I was able to reproduce the Eigen/TractDisplay library installation problem issue in a clean VM. I will investigate and create a patch as soon as possible.

Best,
Isaiah


[2]  

Inline image 1





On Thu, Mar 16, 2017 at 2:12 PM, Jeff Stevenson <[hidden email]> wrote:
Hi isaiah, fyi when the eigen notice pops up the module for fiber tract display is missing. Not sure if that is a coincidence, but without the display module its not usable. Is there a manual workaround?

I tried the latest release and was unable to download any of the diffusion tool kit. Gave script error dialogue. No love.
Jeff


From: Isaiah Norton
Date: Wednesday, March 1, 2017 at 9:28 AM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thanks for the feedback!

Unfortunately, on Linux it looks like SlicerDMRI, UKF, and a number of other modules have empty package download files in the current nightly (tried SlicerRT, TCIABrowser, DSCMRIAnalysis, SlicerPathology, IntensitySegmenter). There are messages in the Slicer error log about empty archives, but regrettably the extension manager doesn't currently provide any prominent error message about this type of install failure.


btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

Not sure about this one -- I believe each version should have its own config sub-folder, and at least on Mac any downloaded extensions are stored inside the version-specific app bundle.

The Eigen notice is present on all platforms but should not affect functionality of either the main DMRI modules or UKF, when they are otherwise installed correctly. I'll see if I can find a way to fix the message.

Best,
Isaiah


On Tue, Feb 21, 2017 at 2:03 PM, Jeff Stevenson <[hidden email]> wrote:
Hi slicer folks, been following the latest module releases of DMRI and UKFT . i tried to download the same dev version today 4.7.0-2017-02-18 r25712.
on my mac the module install fine. on my 14.04 linux workstation i get a dependency error

“the extension Eigen could not be found. the extension
may not work properly.”

tractography display seems not to be installed when this happens, so DMRI/UKFT build on linux still has some issues.

cheers jeff

btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ



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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: slicer DMRI Extensions

Andras Lasso-2

Isaiah, having a monthly snapshot wpuld be great. Would you make all other extensions available for these monthly snapshots? Could you build a barebone installer, too, that doesn't contain any extensions? Would the snapshot be a custom application (unique name, settings, icon, etc.)?

 

Andras

 

From: [hidden email]
Sent: Thursday, March 16, 2017 4:48 PM
To: [hidden email]
Cc: [hidden email]
Subject: Re: [slicer-users] slicer DMRI Extensions

 

Hi Jeff,

Thank you for your patience, I apologize for these problems. Going forward we will be creating "snapshot" packages with SlicerDMRI pre-installed, on a regular basis (~monthly).

We will link to these snapshots as the recommended installation method on our website. The extension will still be available in the nightly too, but in light of various extension download issues [1], we are going to experiment with snapshots as a better way to create a smooth installation process.

To that end: I have created an initial snapshot against the Slicer Linux nightly from 3/12, available to download here:


I tested this on an Ubuntu 14.04 virtualbox VM, and the seeding/display features work as expected (attached screenshot [2]).  I will script up the process and create similar packages for Mac and Windows shortly, and upload to the same location. I hope that this works correctly, but please let me know if not.

Regarding 4.6.2 on Linux, I was able to reproduce the Eigen/TractDisplay library installation problem issue in a clean VM. I will investigate and create a patch as soon as possible.

Best,
Isaiah


[2]  

Inline image 1





On Thu, Mar 16, 2017 at 2:12 PM, Jeff Stevenson <[hidden email]> wrote:
Hi isaiah, fyi when the eigen notice pops up the module for fiber tract display is missing. Not sure if that is a coincidence, but without the display module its not usable. Is there a manual workaround?

I tried the latest release and was unable to download any of the diffusion tool kit. Gave script error dialogue. No love.
Jeff


From: Isaiah Norton
Date: Wednesday, March 1, 2017 at 9:28 AM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thanks for the feedback!

Unfortunately, on Linux it looks like SlicerDMRI, UKF, and a number of other modules have empty package download files in the current nightly (tried SlicerRT, TCIABrowser, DSCMRIAnalysis, SlicerPathology, IntensitySegmenter). There are messages in the Slicer error log about empty archives, but regrettably the extension manager doesn't currently provide any prominent error message about this type of install failure.


btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

Not sure about this one -- I believe each version should have its own config sub-folder, and at least on Mac any downloaded extensions are stored inside the version-specific app bundle.

The Eigen notice is present on all platforms but should not affect functionality of either the main DMRI modules or UKF, when they are otherwise installed correctly. I'll see if I can find a way to fix the message.

Best,
Isaiah


On Tue, Feb 21, 2017 at 2:03 PM, Jeff Stevenson <[hidden email]> wrote:
Hi slicer folks, been following the latest module releases of DMRI and UKFT . i tried to download the same dev version today 4.7.0-2017-02-18 r25712.
on my mac the module install fine. on my 14.04 linux workstation i get a dependency error

“the extension Eigen could not be found. the extension
may not work properly.”

tractography display seems not to be installed when this happens, so DMRI/UKFT build on linux still has some issues.

cheers jeff

btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ



_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
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Re: slicer DMRI Extensions

Jeff Stevenson-2
In reply to this post by Jeff Stevenson-2
Hi isaiah, thanks for the quick followup, I’ll test and let you know if there are any issues. j

From: Isaiah Norton
Date: Thursday, March 16, 2017 at 1:48 PM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thank you for your patience, I apologize for these problems. Going forward we will be creating "snapshot" packages with SlicerDMRI pre-installed, on a regular basis (~monthly).

We will link to these snapshots as the recommended installation method on our website. The extension will still be available in the nightly too, but in light of various extension download issues [1], we are going to experiment with snapshots as a better way to create a smooth installation process.

To that end: I have created an initial snapshot against the Slicer Linux nightly from 3/12, available to download here:


I tested this on an Ubuntu 14.04 virtualbox VM, and the seeding/display features work as expected (attached screenshot [2]).  I will script up the process and create similar packages for Mac and Windows shortly, and upload to the same location. I hope that this works correctly, but please let me know if not.

Regarding 4.6.2 on Linux, I was able to reproduce the Eigen/TractDisplay library installation problem issue in a clean VM. I will investigate and create a patch as soon as possible.

Best,
Isaiah


[2]  

Inline image 1





On Thu, Mar 16, 2017 at 2:12 PM, Jeff Stevenson <[hidden email]> wrote:
Hi isaiah, fyi when the eigen notice pops up the module for fiber tract display is missing. Not sure if that is a coincidence, but without the display module its not usable. Is there a manual workaround?

I tried the latest release and was unable to download any of the diffusion tool kit. Gave script error dialogue. No love.
Jeff


From: Isaiah Norton
Date: Wednesday, March 1, 2017 at 9:28 AM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thanks for the feedback!

Unfortunately, on Linux it looks like SlicerDMRI, UKF, and a number of other modules have empty package download files in the current nightly (tried SlicerRT, TCIABrowser, DSCMRIAnalysis, SlicerPathology, IntensitySegmenter). There are messages in the Slicer error log about empty archives, but regrettably the extension manager doesn't currently provide any prominent error message about this type of install failure.


btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

Not sure about this one -- I believe each version should have its own config sub-folder, and at least on Mac any downloaded extensions are stored inside the version-specific app bundle.

The Eigen notice is present on all platforms but should not affect functionality of either the main DMRI modules or UKF, when they are otherwise installed correctly. I'll see if I can find a way to fix the message.

Best,
Isaiah


On Tue, Feb 21, 2017 at 2:03 PM, Jeff Stevenson <[hidden email]> wrote:
Hi slicer folks, been following the latest module releases of DMRI and UKFT . i tried to download the same dev version today 4.7.0-2017-02-18 r25712.
on my mac the module install fine. on my 14.04 linux workstation i get a dependency error

“the extension Eigen could not be found. the extension
may not work properly.”

tractography display seems not to be installed when this happens, so DMRI/UKFT build on linux still has some issues.

cheers jeff

btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ



_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
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Re: slicer DMRI Extensions

inorton
In reply to this post by inorton
Hi Andras,

Right now I'm aiming for something very simple: to repackage a known-good nightly build with our extensions installed, and uploaded as a GitHub release. I'm not planning to set up a separate build system. Doing repackaging-only should run within the time limits of the free versions of Appveyor (Windows) and Travis (Linux,Mac).

Would you make all other extensions available for these monthly snapshots? 

I'd like to get this going for SlicerDMRI before committing/commenting, but maybe opt-in. I definitely don't want to poll the entire extension index because there is a lot of unmaintained stuff and it will take too long.

Could you build a barebone installer, too, that doesn't contain any extensions?

The corresponding nightly installer for the given snapshot date would be the barebones installer.

Would the snapshot be a custom application (unique name, settings, icon, etc.)?

No. My goal is just a "nightly plus" from a known-good build. I don't want (nor have resources) to duplicate the existing build infrastructure.

Isaiah


On Thu, Mar 16, 2017 at 5:04 PM, Andras Lasso <[hidden email]> wrote:

Isaiah, having a monthly snapshot wpuld be great. Would you make all other extensions available for these monthly snapshots? Could you build a barebone installer, too, that doesn't contain any extensions? Would the snapshot be a custom application (unique name, settings, icon, etc.)?

 

Andras

 

From: [hidden email]
Sent: Thursday, March 16, 2017 4:48 PM
To: [hidden email]
Cc: [hidden email]
Subject: Re: [slicer-users] slicer DMRI Extensions

 

Hi Jeff,

Thank you for your patience, I apologize for these problems. Going forward we will be creating "snapshot" packages with SlicerDMRI pre-installed, on a regular basis (~monthly).

We will link to these snapshots as the recommended installation method on our website. The extension will still be available in the nightly too, but in light of various extension download issues [1], we are going to experiment with snapshots as a better way to create a smooth installation process.

To that end: I have created an initial snapshot against the Slicer Linux nightly from 3/12, available to download here:


I tested this on an Ubuntu 14.04 virtualbox VM, and the seeding/display features work as expected (attached screenshot [2]).  I will script up the process and create similar packages for Mac and Windows shortly, and upload to the same location. I hope that this works correctly, but please let me know if not.

Regarding 4.6.2 on Linux, I was able to reproduce the Eigen/TractDisplay library installation problem issue in a clean VM. I will investigate and create a patch as soon as possible.

Best,
Isaiah


[2]  

Inline image 1





On Thu, Mar 16, 2017 at 2:12 PM, Jeff Stevenson <[hidden email]> wrote:
Hi isaiah, fyi when the eigen notice pops up the module for fiber tract display is missing. Not sure if that is a coincidence, but without the display module its not usable. Is there a manual workaround?

I tried the latest release and was unable to download any of the diffusion tool kit. Gave script error dialogue. No love.
Jeff


From: Isaiah Norton
Date: Wednesday, March 1, 2017 at 9:28 AM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thanks for the feedback!

Unfortunately, on Linux it looks like SlicerDMRI, UKF, and a number of other modules have empty package download files in the current nightly (tried SlicerRT, TCIABrowser, DSCMRIAnalysis, SlicerPathology, IntensitySegmenter). There are messages in the Slicer error log about empty archives, but regrettably the extension manager doesn't currently provide any prominent error message about this type of install failure.


btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

Not sure about this one -- I believe each version should have its own config sub-folder, and at least on Mac any downloaded extensions are stored inside the version-specific app bundle.

The Eigen notice is present on all platforms but should not affect functionality of either the main DMRI modules or UKF, when they are otherwise installed correctly. I'll see if I can find a way to fix the message.

Best,
Isaiah


On Tue, Feb 21, 2017 at 2:03 PM, Jeff Stevenson <[hidden email]> wrote:
Hi slicer folks, been following the latest module releases of DMRI and UKFT . i tried to download the same dev version today 4.7.0-2017-02-18 r25712.
on my mac the module install fine. on my 14.04 linux workstation i get a dependency error

“the extension Eigen could not be found. the extension
may not work properly.”

tractography display seems not to be installed when this happens, so DMRI/UKFT build on linux still has some issues.

cheers jeff

btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ




_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: slicer DMRI Extensions

Steve Pieper-2
Hi Isaiah - 

Just a reminder, the CustomSlicerGenerator already allows you to bundle up whatever extensions you want (and exclude modules you don't want) into a new application that has it's own settings so it doesn't conflict with standard Slicer.  It's pure python and just repackages the binaries from the factory.


It would be great if you could build on that to make your snapshots since it's designed for exactly your scenario.

-Steve

On Thu, Mar 16, 2017 at 6:08 PM, Isaiah Norton <[hidden email]> wrote:
Hi Andras,

Right now I'm aiming for something very simple: to repackage a known-good nightly build with our extensions installed, and uploaded as a GitHub release. I'm not planning to set up a separate build system. Doing repackaging-only should run within the time limits of the free versions of Appveyor (Windows) and Travis (Linux,Mac).

Would you make all other extensions available for these monthly snapshots? 

I'd like to get this going for SlicerDMRI before committing/commenting, but maybe opt-in. I definitely don't want to poll the entire extension index because there is a lot of unmaintained stuff and it will take too long.

Could you build a barebone installer, too, that doesn't contain any extensions?

The corresponding nightly installer for the given snapshot date would be the barebones installer.

Would the snapshot be a custom application (unique name, settings, icon, etc.)?

No. My goal is just a "nightly plus" from a known-good build. I don't want (nor have resources) to duplicate the existing build infrastructure.

Isaiah


On Thu, Mar 16, 2017 at 5:04 PM, Andras Lasso <[hidden email]> wrote:

Isaiah, having a monthly snapshot wpuld be great. Would you make all other extensions available for these monthly snapshots? Could you build a barebone installer, too, that doesn't contain any extensions? Would the snapshot be a custom application (unique name, settings, icon, etc.)?

 

Andras

 

From: [hidden email]
Sent: Thursday, March 16, 2017 4:48 PM


To: [hidden email]
Cc: [hidden email]
Subject: Re: [slicer-users] slicer DMRI Extensions

 

Hi Jeff,

Thank you for your patience, I apologize for these problems. Going forward we will be creating "snapshot" packages with SlicerDMRI pre-installed, on a regular basis (~monthly).

We will link to these snapshots as the recommended installation method on our website. The extension will still be available in the nightly too, but in light of various extension download issues [1], we are going to experiment with snapshots as a better way to create a smooth installation process.

To that end: I have created an initial snapshot against the Slicer Linux nightly from 3/12, available to download here:


I tested this on an Ubuntu 14.04 virtualbox VM, and the seeding/display features work as expected (attached screenshot [2]).  I will script up the process and create similar packages for Mac and Windows shortly, and upload to the same location. I hope that this works correctly, but please let me know if not.

Regarding 4.6.2 on Linux, I was able to reproduce the Eigen/TractDisplay library installation problem issue in a clean VM. I will investigate and create a patch as soon as possible.

Best,
Isaiah


[2]  

Inline image 1





On Thu, Mar 16, 2017 at 2:12 PM, Jeff Stevenson <[hidden email]> wrote:
Hi isaiah, fyi when the eigen notice pops up the module for fiber tract display is missing. Not sure if that is a coincidence, but without the display module its not usable. Is there a manual workaround?

I tried the latest release and was unable to download any of the diffusion tool kit. Gave script error dialogue. No love.
Jeff


From: Isaiah Norton
Date: Wednesday, March 1, 2017 at 9:28 AM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thanks for the feedback!

Unfortunately, on Linux it looks like SlicerDMRI, UKF, and a number of other modules have empty package download files in the current nightly (tried SlicerRT, TCIABrowser, DSCMRIAnalysis, SlicerPathology, IntensitySegmenter). There are messages in the Slicer error log about empty archives, but regrettably the extension manager doesn't currently provide any prominent error message about this type of install failure.


btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

Not sure about this one -- I believe each version should have its own config sub-folder, and at least on Mac any downloaded extensions are stored inside the version-specific app bundle.

The Eigen notice is present on all platforms but should not affect functionality of either the main DMRI modules or UKF, when they are otherwise installed correctly. I'll see if I can find a way to fix the message.

Best,
Isaiah


On Tue, Feb 21, 2017 at 2:03 PM, Jeff Stevenson <[hidden email]> wrote:
Hi slicer folks, been following the latest module releases of DMRI and UKFT . i tried to download the same dev version today 4.7.0-2017-02-18 r25712.
on my mac the module install fine. on my 14.04 linux workstation i get a dependency error

“the extension Eigen could not be found. the extension
may not work properly.”

tractography display seems not to be installed when this happens, so DMRI/UKFT build on linux still has some issues.

cheers jeff

btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

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Re: slicer DMRI Extensions

Jeff Stevenson-2
In reply to this post by Jeff Stevenson-2
Seems to work. Thanks for doing this. Know its a pain. I added UKFT to the mix no problem, got the eigen error but with tractography display already installed, no problem. Awesome! j

From: Isaiah Norton
Date: Thursday, March 16, 2017 at 1:48 PM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thank you for your patience, I apologize for these problems. Going forward we will be creating "snapshot" packages with SlicerDMRI pre-installed, on a regular basis (~monthly).

We will link to these snapshots as the recommended installation method on our website. The extension will still be available in the nightly too, but in light of various extension download issues [1], we are going to experiment with snapshots as a better way to create a smooth installation process.

To that end: I have created an initial snapshot against the Slicer Linux nightly from 3/12, available to download here:


I tested this on an Ubuntu 14.04 virtualbox VM, and the seeding/display features work as expected (attached screenshot [2]).  I will script up the process and create similar packages for Mac and Windows shortly, and upload to the same location. I hope that this works correctly, but please let me know if not.

Regarding 4.6.2 on Linux, I was able to reproduce the Eigen/TractDisplay library installation problem issue in a clean VM. I will investigate and create a patch as soon as possible.

Best,
Isaiah


[2]  

Inline image 1





On Thu, Mar 16, 2017 at 2:12 PM, Jeff Stevenson <[hidden email]> wrote:
Hi isaiah, fyi when the eigen notice pops up the module for fiber tract display is missing. Not sure if that is a coincidence, but without the display module its not usable. Is there a manual workaround?

I tried the latest release and was unable to download any of the diffusion tool kit. Gave script error dialogue. No love.
Jeff


From: Isaiah Norton
Date: Wednesday, March 1, 2017 at 9:28 AM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thanks for the feedback!

Unfortunately, on Linux it looks like SlicerDMRI, UKF, and a number of other modules have empty package download files in the current nightly (tried SlicerRT, TCIABrowser, DSCMRIAnalysis, SlicerPathology, IntensitySegmenter). There are messages in the Slicer error log about empty archives, but regrettably the extension manager doesn't currently provide any prominent error message about this type of install failure.


btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

Not sure about this one -- I believe each version should have its own config sub-folder, and at least on Mac any downloaded extensions are stored inside the version-specific app bundle.

The Eigen notice is present on all platforms but should not affect functionality of either the main DMRI modules or UKF, when they are otherwise installed correctly. I'll see if I can find a way to fix the message.

Best,
Isaiah


On Tue, Feb 21, 2017 at 2:03 PM, Jeff Stevenson <[hidden email]> wrote:
Hi slicer folks, been following the latest module releases of DMRI and UKFT . i tried to download the same dev version today 4.7.0-2017-02-18 r25712.
on my mac the module install fine. on my 14.04 linux workstation i get a dependency error

“the extension Eigen could not be found. the extension
may not work properly.”

tractography display seems not to be installed when this happens, so DMRI/UKFT build on linux still has some issues.

cheers jeff

btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ



_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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Re: slicer DMRI Extensions

inorton
In reply to this post by Jeff Stevenson-2
Thanks for testing, and no problem! Making installs turnkey on all platforms is absolutely the goal; some months/some platforms we slip a bit due to the large number of pieces in play, so it's great to have more eyes and feedback (unlike many open source projects, Slicer doesn't get as much love on Linux these days, sadly, since the vast majority of users are on Windows and Mac).

On Thu, Mar 16, 2017 at 7:08 PM, Jeff Stevenson <[hidden email]> wrote:
Seems to work. Thanks for doing this. Know its a pain. I added UKFT to the mix no problem, got the eigen error but with tractography display already installed, no problem. Awesome! j

From: Isaiah Norton
Date: Thursday, March 16, 2017 at 1:48 PM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thank you for your patience, I apologize for these problems. Going forward we will be creating "snapshot" packages with SlicerDMRI pre-installed, on a regular basis (~monthly).

We will link to these snapshots as the recommended installation method on our website. The extension will still be available in the nightly too, but in light of various extension download issues [1], we are going to experiment with snapshots as a better way to create a smooth installation process.

To that end: I have created an initial snapshot against the Slicer Linux nightly from 3/12, available to download here:


I tested this on an Ubuntu 14.04 virtualbox VM, and the seeding/display features work as expected (attached screenshot [2]).  I will script up the process and create similar packages for Mac and Windows shortly, and upload to the same location. I hope that this works correctly, but please let me know if not.

Regarding 4.6.2 on Linux, I was able to reproduce the Eigen/TractDisplay library installation problem issue in a clean VM. I will investigate and create a patch as soon as possible.

Best,
Isaiah


[2]  

Inline image 1





On Thu, Mar 16, 2017 at 2:12 PM, Jeff Stevenson <[hidden email]> wrote:
Hi isaiah, fyi when the eigen notice pops up the module for fiber tract display is missing. Not sure if that is a coincidence, but without the display module its not usable. Is there a manual workaround?

I tried the latest release and was unable to download any of the diffusion tool kit. Gave script error dialogue. No love.
Jeff


From: Isaiah Norton
Date: Wednesday, March 1, 2017 at 9:28 AM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thanks for the feedback!

Unfortunately, on Linux it looks like SlicerDMRI, UKF, and a number of other modules have empty package download files in the current nightly (tried SlicerRT, TCIABrowser, DSCMRIAnalysis, SlicerPathology, IntensitySegmenter). There are messages in the Slicer error log about empty archives, but regrettably the extension manager doesn't currently provide any prominent error message about this type of install failure.


btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

Not sure about this one -- I believe each version should have its own config sub-folder, and at least on Mac any downloaded extensions are stored inside the version-specific app bundle.

The Eigen notice is present on all platforms but should not affect functionality of either the main DMRI modules or UKF, when they are otherwise installed correctly. I'll see if I can find a way to fix the message.

Best,
Isaiah


On Tue, Feb 21, 2017 at 2:03 PM, Jeff Stevenson <[hidden email]> wrote:
Hi slicer folks, been following the latest module releases of DMRI and UKFT . i tried to download the same dev version today 4.7.0-2017-02-18 r25712.
on my mac the module install fine. on my 14.04 linux workstation i get a dependency error

“the extension Eigen could not be found. the extension
may not work properly.”

tractography display seems not to be installed when this happens, so DMRI/UKFT build on linux still has some issues.

cheers jeff

btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ




_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
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Re: slicer DMRI Extensions

Andras Lasso-2
In reply to this post by inorton

It make sense then to choose a version that corresponds to a nightly build that the factory machines build extensions for.

 

By the way, building all the extensions is really simple and takes about the same time as building Slicer. The difficulty is that you have to set up the build on all platforms

 

Andras

 

From: [hidden email]
Sent: Thursday, March 16, 2017 6:08 PM
To: [hidden email]
Cc: [hidden email]; [hidden email]
Subject: Re: [slicer-users] slicer DMRI Extensions

 

Hi Andras,

Right now I'm aiming for something very simple: to repackage a known-good nightly build with our extensions installed, and uploaded as a GitHub release. I'm not planning to set up a separate build system. Doing repackaging-only should run within the time limits of the free versions of Appveyor (Windows) and Travis (Linux,Mac).

Would you make all other extensions available for these monthly snapshots? 

I'd like to get this going for SlicerDMRI before committing/commenting, but maybe opt-in. I definitely don't want to poll the entire extension index because there is a lot of unmaintained stuff and it will take too long.

Could you build a barebone installer, too, that doesn't contain any extensions?

The corresponding nightly installer for the given snapshot date would be the barebones installer.

Would the snapshot be a custom application (unique name, settings, icon, etc.)?

No. My goal is just a "nightly plus" from a known-good build. I don't want (nor have resources) to duplicate the existing build infrastructure.

Isaiah


On Thu, Mar 16, 2017 at 5:04 PM, Andras Lasso <[hidden email]> wrote:

Isaiah, having a monthly snapshot wpuld be great. Would you make all other extensions available for these monthly snapshots? Could you build a barebone installer, too, that doesn't contain any extensions? Would the snapshot be a custom application (unique name, settings, icon, etc.)?

 

Andras

 

From: [hidden email]
Sent: Thursday, March 16, 2017 4:48 PM
To: [hidden email]
Cc: [hidden email]
Subject: Re: [slicer-users] slicer DMRI Extensions

 

Hi Jeff,

Thank you for your patience, I apologize for these problems. Going forward we will be creating "snapshot" packages with SlicerDMRI pre-installed, on a regular basis (~monthly).

We will link to these snapshots as the recommended installation method on our website. The extension will still be available in the nightly too, but in light of various extension download issues [1], we are going to experiment with snapshots as a better way to create a smooth installation process.

To that end: I have created an initial snapshot against the Slicer Linux nightly from 3/12, available to download here:


I tested this on an Ubuntu 14.04 virtualbox VM, and the seeding/display features work as expected (attached screenshot [2]).  I will script up the process and create similar packages for Mac and Windows shortly, and upload to the same location. I hope that this works correctly, but please let me know if not.

Regarding 4.6.2 on Linux, I was able to reproduce the Eigen/TractDisplay library installation problem issue in a clean VM. I will investigate and create a patch as soon as possible.

Best,
Isaiah


[2]  

Inline image 1





On Thu, Mar 16, 2017 at 2:12 PM, Jeff Stevenson <[hidden email]> wrote:
Hi isaiah, fyi when the eigen notice pops up the module for fiber tract display is missing. Not sure if that is a coincidence, but without the display module its not usable. Is there a manual workaround?

I tried the latest release and was unable to download any of the diffusion tool kit. Gave script error dialogue. No love.
Jeff


From: Isaiah Norton
Date: Wednesday, March 1, 2017 at 9:28 AM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thanks for the feedback!

Unfortunately, on Linux it looks like SlicerDMRI, UKF, and a number of other modules have empty package download files in the current nightly (tried SlicerRT, TCIABrowser, DSCMRIAnalysis, SlicerPathology, IntensitySegmenter). There are messages in the Slicer error log about empty archives, but regrettably the extension manager doesn't currently provide any prominent error message about this type of install failure.


btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

Not sure about this one -- I believe each version should have its own config sub-folder, and at least on Mac any downloaded extensions are stored inside the version-specific app bundle.

The Eigen notice is present on all platforms but should not affect functionality of either the main DMRI modules or UKF, when they are otherwise installed correctly. I'll see if I can find a way to fix the message.

Best,
Isaiah


On Tue, Feb 21, 2017 at 2:03 PM, Jeff Stevenson <[hidden email]> wrote:
Hi slicer folks, been following the latest module releases of DMRI and UKFT . i tried to download the same dev version today 4.7.0-2017-02-18 r25712.
on my mac the module install fine. on my 14.04 linux workstation i get a dependency error

“the extension Eigen could not be found. the extension
may not work properly.”

tractography display seems not to be installed when this happens, so DMRI/UKFT build on linux still has some issues.

cheers jeff

btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ




_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
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Re: slicer DMRI Extensions

Andras Lasso-2
In reply to this post by inorton

Would it work for you if we picked a nightly version once in every 1-2 months (that has no known major issues) and build all extensions for that every night?

 

Stable builds do almost exactly this except:

  • Created yearly instead of monthly
  • Download is very slow

 

Shouldn't we try to improve stable builds instead of building a limited build infrastructure in parallel? I'm afraid introducing additional build infrastructures would be more work overall, we would loose download stats, and confuse users. Or at least coordinate these private builds: make them binary compatible, collect download stats in one location, show all download links on the official Slicer download page, etc.

 

Andras

 

From: [hidden email]
Sent: Friday, March 17, 2017 10:23 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]
Subject: RE: [slicer-users] slicer DMRI Extensions

 

It make sense then to choose a version that corresponds to a nightly build that the factory machines build extensions for.

 

By the way, building all the extensions is really simple and takes about the same time as building Slicer. The difficulty is that you have to set up the build on all platforms

 

Andras

 

From: [hidden email]
Sent: Thursday, March 16, 2017 6:08 PM
To: [hidden email]
Cc: [hidden email]; [hidden email]
Subject: Re: [slicer-users] slicer DMRI Extensions

 

Hi Andras,

Right now I'm aiming for something very simple: to repackage a known-good nightly build with our extensions installed, and uploaded as a GitHub release. I'm not planning to set up a separate build system. Doing repackaging-only should run within the time limits of the free versions of Appveyor (Windows) and Travis (Linux,Mac).

Would you make all other extensions available for these monthly snapshots? 

I'd like to get this going for SlicerDMRI before committing/commenting, but maybe opt-in. I definitely don't want to poll the entire extension index because there is a lot of unmaintained stuff and it will take too long.

Could you build a barebone installer, too, that doesn't contain any extensions?

The corresponding nightly installer for the given snapshot date would be the barebones installer.

Would the snapshot be a custom application (unique name, settings, icon, etc.)?

No. My goal is just a "nightly plus" from a known-good build. I don't want (nor have resources) to duplicate the existing build infrastructure.

Isaiah


On Thu, Mar 16, 2017 at 5:04 PM, Andras Lasso <[hidden email]> wrote:

Isaiah, having a monthly snapshot wpuld be great. Would you make all other extensions available for these monthly snapshots? Could you build a barebone installer, too, that doesn't contain any extensions? Would the snapshot be a custom application (unique name, settings, icon, etc.)?

 

Andras

 

From: [hidden email]
Sent: Thursday, March 16, 2017 4:48 PM
To: [hidden email]
Cc: [hidden email]
Subject: Re: [slicer-users] slicer DMRI Extensions

 

Hi Jeff,

Thank you for your patience, I apologize for these problems. Going forward we will be creating "snapshot" packages with SlicerDMRI pre-installed, on a regular basis (~monthly).

We will link to these snapshots as the recommended installation method on our website. The extension will still be available in the nightly too, but in light of various extension download issues [1], we are going to experiment with snapshots as a better way to create a smooth installation process.

To that end: I have created an initial snapshot against the Slicer Linux nightly from 3/12, available to download here:


I tested this on an Ubuntu 14.04 virtualbox VM, and the seeding/display features work as expected (attached screenshot [2]).  I will script up the process and create similar packages for Mac and Windows shortly, and upload to the same location. I hope that this works correctly, but please let me know if not.

Regarding 4.6.2 on Linux, I was able to reproduce the Eigen/TractDisplay library installation problem issue in a clean VM. I will investigate and create a patch as soon as possible.

Best,
Isaiah


[2]  

Inline image 1





On Thu, Mar 16, 2017 at 2:12 PM, Jeff Stevenson <[hidden email]> wrote:
Hi isaiah, fyi when the eigen notice pops up the module for fiber tract display is missing. Not sure if that is a coincidence, but without the display module its not usable. Is there a manual workaround?

I tried the latest release and was unable to download any of the diffusion tool kit. Gave script error dialogue. No love.
Jeff


From: Isaiah Norton
Date: Wednesday, March 1, 2017 at 9:28 AM
To: Jeff Stevenson
Cc: SPL Slicer Users
Subject: Re: [slicer-users] slicer DMRI Extensions

Hi Jeff,

Thanks for the feedback!

Unfortunately, on Linux it looks like SlicerDMRI, UKF, and a number of other modules have empty package download files in the current nightly (tried SlicerRT, TCIABrowser, DSCMRIAnalysis, SlicerPathology, IntensitySegmenter). There are messages in the Slicer error log about empty archives, but regrettably the extension manager doesn't currently provide any prominent error message about this type of install failure.


btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

Not sure about this one -- I believe each version should have its own config sub-folder, and at least on Mac any downloaded extensions are stored inside the version-specific app bundle.

The Eigen notice is present on all platforms but should not affect functionality of either the main DMRI modules or UKF, when they are otherwise installed correctly. I'll see if I can find a way to fix the message.

Best,
Isaiah


On Tue, Feb 21, 2017 at 2:03 PM, Jeff Stevenson <[hidden email]> wrote:
Hi slicer folks, been following the latest module releases of DMRI and UKFT . i tried to download the same dev version today 4.7.0-2017-02-18 r25712.
on my mac the module install fine. on my 14.04 linux workstation i get a dependency error

“the extension Eigen could not be found. the extension
may not work properly.”

tractography display seems not to be installed when this happens, so DMRI/UKFT build on linux still has some issues.

cheers jeff

btw also found the newer releases crash when extension manager is called when older versions are in the .config folder.
moving them out solves the problem with latest releases after feb 1, tho inconvenient.

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ




_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ