Hello Yap,
sorry for the long wait, somehow I didn't realize you were waiting for an
answer.
Ok, so you stumbled on an outstanding bug of the 0.9 release (which has been
fixed in the development repository).
Basically, you have to go in the vmtk install location (could be /user/local if
you compiled from source, or /Applications/vmtk.app/Contents/Resources/
if you are running off the binary version) and look into
lib/vmtk/vmtk/vmtkcenterlinegeometry.py
relative to that directory. This is where all the scripts reside.
The bug can be fixed by editing vmtkcenterlinegeometry.py and adding
centerlineGeometry.SetLengthArrayName('Length')
centerlineGeometry.SetTortuosityArrayName('Tortuosity')
after the line
centerlineGeometry = vtkvmtk.vtkvmtkCenterlineGeometry()
Hope this solves it
Luca
On Sep 21, 2011, at 6:24 PM, Yap, Choon Hwai wrote:
> Luca,
>
> sorry for the multiple emails, I would also like to find out why I'm getting
> a blank .dat file with vmtkcenterlinegeometry with command,
>
> vmtkcenterlinegeometry -ifile centerline.vtp -smoothing 1 -ofile
> centerline.dat
>
> the error message is that the LengthArrayName is not specified,
>
> is there a way to look into the codes and figure all these out by myself?
>
> thanks!
>
> regards,
> Yap
>
>
> ----- Original Message -----
> From: "Luca Antiga" <luca.ant...@gmail.com>
> To: "Choon Hwai Yap" <cy...@bme.gatech.edu>
> Cc: vmtk-users@lists.sourceforge.net
> Sent: Wednesday, September 21, 2011 2:46:13 AM
> Subject: Re: [vmtk-users] error saving file
>
> Hi Yap,
> I am running off a Mac myself and didn't stumble on this one. A few quick
> questions:
> What OS are you running? (Snow Leopard, Lion?)
> Are you using a compiled vmtk or the one from the binary package?
> Are you running the pipe from PypePad or from the terminal?
>
> Luca
>
>
> On Sep 21, 2011, at 5:32 AM, Yap, Choon Hwai wrote:
>
>> Hi all,
>>
>> I'm running levelsetsegementation on the Mac, and encounter this error
>> everytime I save an output:
>>
>> ** __NSAutoreleaseFreedObject(): release of previously deallocated object
>> (0x1294ca0) ignored
>>
>> and the next time I run the same command, it gives a whole lot of errors
>> with allocating memory.
>>
>> Any help will be greatly appreciated..!
>>
>> regards,
>> Yap
>>
>>
>> ----- Original Message -----
>> From: vmtk-users-requ...@lists.sourceforge.net
>> To: vmtk-users@lists.sourceforge.net
>> Sent: Tuesday, September 13, 2011 3:50:40 AM
>> Subject: vmtk-users Digest, Vol 47, Issue 2
>>
>> Send vmtk-users mailing list submissions to
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>>
>>
>> Today's Topics:
>>
>> 1. Help with VMTK imagewriter (VITALY KHEYFETS)
>> 2. Re: Help with VMTK imagewriter (ido yerushalmy)
>> 3. Re: Help with VMTK imagewriter (Luca Antiga)
>> 4. Compiling VMTK for Slicer 3D (ido yerushalmy)
>> 5. Re: Compiling VMTK for Slicer 3D (Luca Antiga)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 7 Sep 2011 15:26:46 -0500
>> From: VITALY KHEYFETS <vitaly.kheyf...@utsa.edu>
>> Subject: [vmtk-users] Help with VMTK imagewriter
>> To: <vmtk-users@lists.sourceforge.net>
>> Message-ID:
>> <67f727f9dc5673439f2a984d7bdfa85a510...@lapis1604.utsarr.net>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hello,
>>
>> This may be a dumb question, but I am trying to read DICOM images and create
>> a *.vti output file.
>>
>> This is my script: vmtkimagereader -ifile C:\DICOM_Imag\Normal_PA_Clean\IM1
>> --pipe vmtkimagewriter -ofile image_volume.vti
>>
>> I can read and view the images, but when running this code I can't find the
>> file: image_volume.vti
>>
>> What directory should that be saved in? Or is that just stored in memory?
>>
>> Thanks,
>>
>> Vitaly
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 8 Sep 2011 08:08:56 +0300
>> From: ido yerushalmy <ido.yerusha...@gmail.com>
>> Subject: Re: [vmtk-users] Help with VMTK imagewriter
>> To: VITALY KHEYFETS <vitaly.kheyf...@utsa.edu>
>> Cc: vmtk-users@lists.sourceforge.net
>> Message-ID:
>> <CAL8jJRFV6=KS4_E2VMY5xxqteLx7U73NMn83=r3yfpz1f9n...@mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi Vitaly,
>> If I'm not mistaking, the file will be saved in the directory from which you
>> are running PypePad.
>> Or, if you defined an environment variable for VMTK, in the directory from
>> which you launched PypePad.
>>
>> Hopes this helps,
>> Ido
>>
>> On Wed, Sep 7, 2011 at 11:26 PM, VITALY KHEYFETS
>> <vitaly.kheyf...@utsa.edu>wrote:
>>
>>> **
>>>
>>> Hello,
>>>
>>> This may be a dumb question, but I am trying to read DICOM images and
>>> create a *.vti output file.
>>>
>>> This is my script: vmtkimagereader -ifile C:\DICOM_Imag\Normal_PA_Clean\IM1
>>> --pipe vmtkimagewriter -ofile image_volume.vti
>>>
>>> I can read and view the images, but when running this code I can't find the
>>> file: image_volume.vti
>>>
>>> What directory should that be saved in? Or is that just stored in memory?
>>>
>>> Thanks,
>>>
>>> Vitaly
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Using storage to extend the benefits of virtualization and iSCSI
>>> Virtualization increases hardware utilization and delivers a new level of
>>> agility. Learn what those decisions are and how to modernize your storage
>>> and backup environments for virtualization.
>>> http://www.accelacomm.com/jaw/sfnl/114/51434361/
>>> _______________________________________________
>>> vmtk-users mailing list
>>> vmtk-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>
>>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Fri, 9 Sep 2011 09:07:30 +0200
>> From: Luca Antiga <luca.ant...@orobix.com>
>> Subject: Re: [vmtk-users] Help with VMTK imagewriter
>> To: ido yerushalmy <ido.yerusha...@gmail.com>
>> Cc: vmtk-users@lists.sourceforge.net
>> Message-ID: <b153b698-15d3-45e9-9d3c-75b4b7a2e...@orobix.com>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Hi Vitaly,
>> in addition to Ido's suggestion, you can of course specify the full output
>> path at the command line:
>>
>> vmtkimagereader -ifile C:\DICOM_Imag\Normal_PA_Clean\IM1 --pipe
>> vmtkimagewriter -ofile C:\DICOM_Imag\image_volume.vti
>>
>> Best regards
>>
>> Luca
>>
>>
>> On Sep 8, 2011, at 7:08 AM, ido yerushalmy wrote:
>>
>>> Hi Vitaly,
>>> If I'm not mistaking, the file will be saved in the directory from which
>>> you are running PypePad.
>>> Or, if you defined an environment variable for VMTK, in the directory from
>>> which you launched PypePad.
>>>
>>> Hopes this helps,
>>> Ido
>>>
>>> On Wed, Sep 7, 2011 at 11:26 PM, VITALY KHEYFETS <vitaly.kheyf...@utsa.edu>
>>> wrote:
>>> Hello,
>>>
>>> This may be a dumb question, but I am trying to read DICOM images and
>>> create a *.vti output file.
>>>
>>> This is my script: vmtkimagereader -ifile C:\DICOM_Imag\Normal_PA_Clean\IM1
>>> --pipe vmtkimagewriter -ofile image_volume.vti
>>>
>>> I can read and view the images, but when running this code I can't find the
>>> file: image_volume.vti
>>>
>>> What directory should that be saved in? Or is that just stored in memory?
>>>
>>> Thanks,
>>>
>>> Vitaly
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Using storage to extend the benefits of virtualization and iSCSI
>>> Virtualization increases hardware utilization and delivers a new level of
>>> agility. Learn what those decisions are and how to modernize your storage
>>> and backup environments for virtualization.
>>> http://www.accelacomm.com/jaw/sfnl/114/51434361/
>>> _______________________________________________
>>> vmtk-users mailing list
>>> vmtk-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Doing More with Less: The Next Generation Virtual Desktop
>>> What are the key obstacles that have prevented many mid-market businesses
>>> from deploying virtual desktops? How do next-generation virtual desktops
>>> provide companies an easier-to-deploy, easier-to-manage and more affordable
>>> virtual desktop
>>> model.http://www.accelacomm.com/jaw/sfnl/114/51426474/_______________________________________________
>>> vmtk-users mailing list
>>> vmtk-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Sun, 11 Sep 2011 16:23:07 +0300
>> From: ido yerushalmy <ido.yerusha...@gmail.com>
>> Subject: [vmtk-users] Compiling VMTK for Slicer 3D
>> To: vmtk-users@lists.sourceforge.net
>> Message-ID:
>> <CAL8jJRF=enntqqsyckfh_zbk8-wabtselsfhjaj-k5ovkbn...@mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi all,
>> I am using VMTK as a module of Slicer 3D (http://www.slicer.org/).
>> I downloaded a few months ago the source code together with Cmake files that
>> compile into a set of* DLLs that can be used from within Slicer*.
>> I know the code is the same as the standalone version of VMTK, but the
>> Cmakes are built differently.
>>
>> I'm now looking for this package again and just unable to find it, could
>> anyone remind me where to look?
>>
>> Best regards,
>> Ido
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Tue, 13 Sep 2011 09:50:28 +0200
>> From: Luca Antiga <luca.ant...@orobix.com>
>> Subject: Re: [vmtk-users] Compiling VMTK for Slicer 3D
>> To: ido yerushalmy <ido.yerusha...@gmail.com>
>> Cc: vmtk-users@lists.sourceforge.net
>> Message-ID: <de262cf5-291f-439e-b07a-9ed085fdd...@gmail.com>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Hello Ido,
>> this is where you should look
>>
>> http://www.nitrc.org/projects/slicervmtklvlst/
>>
>> but I just noticed that you posted messages on the forum there, so you
>> probably already know...
>>
>> There is a great effort around vmtk in 3D Slicer 4 as well. Daniel Haehn is
>> in any case the person to contact.
>>
>> Best regards
>>
>> Luca
>>
>>
>> On Sep 11, 2011, at 3:23 PM, ido yerushalmy wrote:
>>
>>> Hi all,
>>> I am using VMTK as a module of Slicer 3D (http://www.slicer.org/).
>>> I downloaded a few months ago the source code together with Cmake files
>>> that compile into a set of DLLs that can be used from within Slicer.
>>> I know the code is the same as the standalone version of VMTK, but the
>>> Cmakes are built differently.
>>>
>>> I'm now looking for this package again and just unable to find it, could
>>> anyone remind me where to look?
>>>
>>> Best regards,
>>> Ido
>>> ------------------------------------------------------------------------------
>>> Using storage to extend the benefits of virtualization and iSCSI
>>> Virtualization increases hardware utilization and delivers a new level of
>>> agility. Learn what those decisions are and how to modernize your storage
>>> and backup environments for virtualization.
>>> http://www.accelacomm.com/jaw/sfnl/114/51434361/_______________________________________________
>>> vmtk-users mailing list
>>> vmtk-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
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>>
>> ------------------------------------------------------------------------------
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>>
>> End of vmtk-users Digest, Vol 47, Issue 2
>> *****************************************
>>
>> ------------------------------------------------------------------------------
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threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
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