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IDProjectCategoryView StatusLast Update
0002780Slicer4Module BRAINSpublic2013-07-05 13:09
Reporterpohl Assigned Tohjmjohnson  
PrioritynormalSeverityminorReproducibilityhave not tried
Status closedResolutionsuspended 
Product Version 
Target VersionSlicer 4.3.0Fixed in VersionSlicer 4.3.0 
Summary0002780: BRAINSFit takes a long time to run on windows
Description

As reported by Kilian, it takes 5 minutes on Linux but much longer on windows (> 15mins). Is there any thing that could be done ?

The data and exact command line to run BRAINSFit are available in the archive referenced in the following note: http://www.na-mic.org/Bug/view.php?id=2741#c7331

TagsNo tags attached.

Relationships

child of 0002741 closedpohl Fix EMSegCLTask{HumanEye, MRIHumanBrainExp}_BRAINS_small failing on windows 

Activities

jcfr

jcfr

2013-04-05 12:32

administrator   ~0008325

Reminder sent to: pohl

Hi Kilian,

Is this still an issue ? After solving the current issue related to BRAINSFit, could you check if the module is still slow ? Now, we are using ITKv4, it should be faster ?

hjmjohnson

hjmjohnson

2013-04-22 13:07

developer   ~0008461

Is the windows build a Debug or a Release build? In debug mode, ITK registration can be very slow. If a release build on windows is still slow, then we would need to determine if there are windows threading issues coming into play.

pohl

pohl

2013-04-22 13:51

developer   ~0008462

I do not have a windows build so I cannot check if it is still an issue

jcfr

jcfr

2013-04-22 13:54

administrator   ~0008463

Last edited: 2013-04-22 14:00

Would it be possible to look at the execution time associated with an existing test ?

If a test can be used to have an idea of the registration time, we could simply look at the test result reported on the factory.

Operating system: Windows 32 and 64 bits

pohl

pohl

2013-04-22 13:57

developer   ~0008464

on what operating system ? I can do it on an ubuntu machine

hjmjohnson

hjmjohnson

2013-07-05 07:27

developer   ~0008864

This issue seems to keep coming up as a problem, but there is no profiling information given. Requests have been made to determine if this is a Debug/Release issue without response.

It seems that no one has the resources to determine what is actually the problem.

Finally, the switch over to ITKv4 addressed several threading issues in the registration framework used by BRAINS, and it MAY have been related to those potential threading bugs that only reared its head on windows.

I don't know how to move forward on this issue without better external support.

hjmjohnson

hjmjohnson

2013-07-05 11:36

developer   ~0008870

-----Original Message-----
From: Ron Kikinis <kikinis@bwh.harvard.edu>
Reply-To: Ron Kikinis <kikinis@bwh.harvard.edu>
Date: Friday, July 5, 2013 2:25 PM
To: Hans Johnson <hans-johnson@uiowa.edu>, Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>, Steve Pieper <pieper@bwh.harvard.edu>, Kilian Pohl <pohl.kilian@gmail.com>
Subject: 0002780: BRAINSFit takes a long time to run on windows - Mantis

http://na-mic.org/Bug/view.php?id=2780

Hi,

I ran brainsfit on both win and mac.
Mac: 8 core 8 gig os 10.8.4
win: 64b, 4 core 4 gig on vmware fusion

I used the same data (meningeomas from the sample data). Same moving and
fixed. Virtually same time to run.

Ron

--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis

jcfr

jcfr

2013-07-05 13:09

administrator   ~0008871

Please, re-open if this is still an issue.

Issue History

Date Modified Username Field Change
2012-11-21 05:21 jcfr New Issue
2012-11-21 05:21 jcfr Status new => assigned
2012-11-21 05:21 jcfr Assigned To => hjmjohnson
2012-11-21 05:21 jcfr Target Version => Slicer 4.2.2
2012-11-21 05:21 jcfr Relationship added child of 0002741
2012-12-07 17:59 jcfr Target Version Slicer 4.2.2 => Slicer 4.2.3
2013-02-12 09:37 jcfr Target Version Slicer 4.2.3 => Slicer 4.3.0
2013-04-05 12:32 jcfr Note Added: 0008325
2013-04-22 13:07 hjmjohnson Note Added: 0008461
2013-04-22 13:18 jcfr Reporter jcfr => pohl
2013-04-22 13:51 pohl Note Added: 0008462
2013-04-22 13:54 jcfr Note Added: 0008463
2013-04-22 13:57 pohl Note Added: 0008464
2013-04-22 14:00 jcfr Note Edited: 0008463
2013-04-22 14:00 jcfr Note Edited: 0008463
2013-07-05 07:27 hjmjohnson Note Added: 0008864
2013-07-05 07:27 hjmjohnson Status assigned => resolved
2013-07-05 07:27 hjmjohnson Resolution open => suspended
2013-07-05 11:36 hjmjohnson Note Added: 0008870
2013-07-05 13:09 jcfr Note Added: 0008871
2013-07-05 13:09 jcfr Status resolved => closed
2013-07-05 13:09 jcfr Fixed in Version => Slicer 4.3.0