NITRC JIST: Java Image Science Toolkit Forum: help

Module Failed in an Ungraceful Manner. Please contact the developer with the following message.

lingzhong Fan — Thu, 28 Mar 2019 9:54:00 GMT

Parallel pool using the 'local' profile is shutting down.
cli ####################################################################
cli Initializing MIPAV/JIST Framework
cli ####################################################################
cli Interpretting command line arguments
cli ####################################################################
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusion
inAtlas = /DATA/251/lzfan/Cere_Project/cerlobule_seg_release_06_01_2016/result_lzfan_AD/1_NC001/mulreg_masked_02atlas/atlas01totest_deformed_label.nii.gz;/DATA/251/lzfan/Cere_Project/cerlobule_seg_release_06_01_2016/result_lzfan_AD/1_NC001/mulreg_masked_02atlas/atlas02totest_deformed_label.nii.gz
inTarget = /DATA/251/lzfan/Cere_Project/cerlobule_seg_release_06_01_2016/result_lzfan_AD/1_NC001/masked_scan.nii.gz
inAtlas2 = /DATA/251/lzfan/Cere_Project/cerlobule_seg_release_06_01_2016/result_lzfan_AD/1_NC001/mulreg_masked_02atlas/atlas01totest_deformed_Scan.nii.gz;/DATA/251/lzfan/Cere_Project/cerlobule_seg_release_06_01_2016/result_lzfan_AD/1_NC001/mulreg_masked_02atlas/atlas02totest_deformed_Scan.nii.gz
inHierarchy = = None
inProbability = = None
inOutput = = None
inOutput2 = = None
inConsensus = 0.900000
inPrior = Voxelwise
inConvergence = 0.000100
inMaximum = 100
inWindow = 5
inWindow2 = 5
inWindow3 = 5
inWindow4 = 0
inBias = 0.200000
inAugment = = false
inWeighting = MSD
inSearch = 2
inSearch2 = 2
inSearch3 = 2
inSearch4 = 0
inPatch = 2
inPatch2 = 2
inPatch3 = 2
inPatch4 = 0
inSearch5 = 1.500000e+00
inSearch6 = 1.500000e+00
inSearch7 = 1.500000e+00
inSearch8 = 0
inDifference = 0.150000
inGlobal = 0.000000
inLocal = 0.000000
inUse = true
inSelection = Jaccard
inSelection2 = 0.050000
inNumber = 150
outLabel = /DATA/251/lzfan/Cere_Project/cerlobule_seg_release_06_01_2016/result_lzfan_AD/1_NC001/NLstaple_label_masked_02atlas.nii.gz
outPerformance = =
outPerformance2 = = Performance Level Parameters Volume
outLabel2 = =
outLabel3 = = Label Probabilities Volume
outProc = /DATA/251/lzfan
cli ####################################################################
*** Determining appropriate type for the observation object. ***
-> Using ObservationVolumePartial.
+++ Initializing Generic Observation Base +++
+++ Initializing Label Observations (Partial Type) +++
+++ Initializing Generic Observation Base +++
+++ Initializing Label Observations (Volume Type) +++
-> Attempting to determine valid cropping region (found 2 label images)
[=+]
Module Failed in an Ungraceful Manner. Please contact the developer with the following message.
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusionRuntime Exception:null
edu.vanderbilt.masi.algorithms.labelfusion.ObservationBase.determine_cropping_information(ObservationBase.java:243)
edu.vanderbilt.masi.algorithms.labelfusion.ObservationVolume.(ObservationVolume.java:28)
edu.vanderbilt.masi.algorithms.labelfusion.ObservationVolumePartial.(ObservationVolumePartial.java:61)
edu.vanderbilt.masi.plugins.labelfusion.AbstractStatisticalFusionPlugin$AbstractExecuteWrapper.get_observation_type(AbstractStatisticalFusionPlugin.java:414)
edu.vanderbilt.masi.plugins.labelfusion.AbstractStatisticalFusionPlugin$AbstractExecuteWrapper.execute(AbstractStatisticalFusionPlugin.java:348)
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusion.execute(PluginStatisticalFusion.java:66)
edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm.runAlgorithm(ProcessingAlgorithm.java:337)
edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm.runAlgorithm(ProcessingAlgorithm.java:321)
edu.jhu.ece.iacl.jist.cli.run.main(run.java:100)
---------- Performance Summary ----------
1) Algorithm Calculation -- ELAPSED TIME: Actual: 0.04 sec / CPU: 0.03 sec

TOTAL ELAPSED TIME: Actual: 0.04 sec / CPU: 0.03 sec
CURRENT MEMORY: Used 90 MB, Free 1841 MB, Total 1932 MB
Error: IOException on GZIPInputStream for NLstaple_label_masked_02atlas.nii.gz
ans =
1
Error using gunzip>gunzipwrite (line 209)
File "/DATA/251/lzfan/Cere_Project/cerlobule_seg_release_06_01_2016/result_lzfan_AD/1_NC001/NLstaple_label_masked_02atlas.nii.gz" is
not in GZIP format.

No output in Lesion toads

butlerj3 — Thu, 11 Oct 2018 14:21:32 GMT

Hope this reaches you well. I am attempting to run lesion toads on my desktop. I am running to an issue where no output images are being generated when I run this algorithm.

I have
input my skull stripped T1 and FLAIR images
Used the lesiontoads-12obj.txt files for the atlases
Designated that the output images should be of hard segmentation+memberships
The rest is what was provided as default settings.
Is there an issue on my end to why this is not giving the outputs I am looking for?
Could you please lend a helping hand?
Thank you

RE: JIST installation problem

Bennett Landman — Sun, 11 Sep 2016 20:03:59 GMT

I was just made aware of these issues. Sorry that I didnt see the messages easier.

On OS X 10.11.6, I just downloaded:
** MIPAV Nightly OS X - https://mipav.cit.nih.gov/download.php 2016.09.11
** http://masijenkins.vuse.vanderbilt.edu:8080/job/Build%20JIST-CRUISE/mipav=%2Fshare%2Fhudson%2Fmipav-nightly/lastSuccessfulBuild/artifact/jars/JIST-CRUISE-2016Sep11-12-06PM.jar

I ran the install.app with "open" and set the memory to 4GB with a destination of ~/mipavNightly.

Mipav reported: Version: 7.3.0-2016-09-11 (2016-09-11)

I went to Plugins -> Install for the jar file, but it reported no plugins found. Restarting MIPAV did not help.

I looked in ~/mipav/plugins (yes, not mipavNightly), but there were no files. I run unzip to extract the jar file to ~/mipav/plugins with overwrite all (for duplicate "license.txt" files.

I restarted mipav and everything works. I've filed a bug report with the MIPAV folks to let them know that the plugin install on mac isn't working.

Does this help?

In the future, please e-mail me directly if a response does not occur in a reasonable amount of time on the forum. I'll still respond here so that the conversations are archived and searchable, but... sometime e-mail filters do not exactly work as intended and I can miss e-mails.

Best,
Bennett

RE: Totally lost

Andrew Plassard — Wed, 15 Jun 2016 13:44:42 GMT

If you want a GUI for JIST, there are several options within the MIPAV plugin depending on what you do.

The JIST CLI is also installed when you install the JIST plugin into MIPAV. You will just need to follow the tutorial I sent before to understand how it works. PyJIST is a simplification of the CLI commands to hide things like setting the java class path.

RE: Totally lost

Ottar Gislason — Wed, 15 Jun 2016 12:04:18 GMT

Thanks for the response Andrew,

So there's no sort of standalone client for JIST? I was operating under the impression that I should be able to find some sort of client so no wonder I was confused.

To answer your question as to what I plan on doing, I honestly have no idea. I just started as an research assistant and was instructed to install all sorts of neuroimaging related stuff but my boss isn't in the country for another week so I'm just sort of blundering my way through.

I have already installed the JIST plugin into MIPAV and it appears to work. So my next step would be to install the CLI? Or is that included automatically? Does PyJIST have a GUI or is it just to simplify the CLI commands?

RE: Totally lost

Andrew Plassard — Wed, 15 Jun 2016 11:33:13 GMT

Hi Ottar,
What are you looking to do with JIST? That will help us point you in the right direction.

You most likely will need to download this version of JIST http://www.nitrc.org/frs/download.php/7248/JIST-2014Dec12-03-34PM.jar, which is the version 3.2 release, and install it into MIPAV following http://www.nitrc.org/plugins/mwiki/index.php/jist:Install.

JIST typically needs to be installed in MIPAV to run, but what it sounds like you want is the command line interface (http://www.nitrc.org/plugins/mwiki/index.php/jist:CommandLineInterface). This is also wrapped nicely in PyJIST (http://www.nitrc.org/plugins/mwiki/index.php/jist:PyJIST).

Hope that helps!
Andrew

Totally lost

Ottar Gislason — Wed, 15 Jun 2016 10:42:22 GMT

I'm trying to install JIST on an ubuntu machine, but I'm not even quite sure of what JIST is/does.

I've installed it as a plugin for MIPAV, but I was instructed to install it also as a standalone. My problem is I'm not really familiar at all with any of this software and it's unclear to me what's what. On the downloads page I see mostly stuff which is marked as MIPAV bundles, which is what I set up as a plugin. But then there's the JIST 2.0 stuff which I guess is probably the standalone, but it's from 2010.. is that normal? I tried downloading it but when I try to execute the .jar file it says its not an executable and is "not marked as executable" and something about executable bits.

If anyone can point me in the right direction it would be greatly appreciated.

Sorry for my ignorance, I'm just a research assistant newbie with limited linux experience and essentially zero neuro/image experience.

RE: JIST installation problem

Seongjin Choi — Thu, 25 Feb 2016 2:18:47 GMT

I found that the error message is misleading. After closing and launching MIPAV again, all the plugins appear on Windows 10. However, the plugins, JIST-CRUISE and others, are still not properly installed on Mac (Yosemite). As recommended elsewhere, I copied all the plugins directly into the 'plugins' folder under /mipav/ then the plugins appears but they don't appear right. It appears as file name, e.g., JIST-CRUISE-2014Dec12-03-37PM.jar.

JIST installation problem

Seongjin Choi — Tue, 02 Feb 2016 4:12:37 GMT

I tried to install JIST (v.3.2) after the installation of MIPAV (7.0+). I followed the instructions and the installation process ended up with an error message, "No plugins were installed, please select valid MIPAV plugin files". I reinstalled MIPAV and tried again, however, the results were identical. I tried on both a Mac (Yosemite) and a Windows 10 laptops. On both computers, the error messages were identical. To make it sure, I tried other plugins such as TOADS-CRUISE. The results were identical.

RE: SPECTRE2010

aaron_carass — Sat, 05 Dec 2015 0:42:36 GMT

Also MIPAV 5.4.2 is old (March or April 2012). JIST 2.0 is not much better.

Aaron