slicer-users Digest

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

slicer-users Digest

Артем Никифоров
What does it meen this message? 
I am the 9th sender?


-------- Пересылаемое сообщение --------
От кого: [hidden email]
Кому: [hidden email]
Дата: Четверг, 26 января 2017, 19:00 +02:00
Тема: slicer-users Digest, Vol 139, Issue 24

Send slicer-users mailing list submissions to
[hidden email]

To subscribe or unsubscribe via the World Wide Web, visit
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
or, via email, send a message with subject or body 'help' to
[hidden email]

You can reach the person managing the list at
[hidden email]

When replying, please edit your Subject line so it is more specific
than "Re: Contents of slicer-users digest..."


Today's Topics:

   1. Re: Fwd: TCIA connection (Andrey Fedorov)
   2. Re: Fwd: TCIA connection (F?lix Navarro Guirado)
   3. Re: Fwd: TCIA connection (Andrey Fedorov)
   4. Re: Extract Skull from MRI image (Felix)
   5. delete fibers manually (Marlene Wigand)
   6. Re: delete fibers manually (Rutvij Kotecha)
   7. Re: delete fibers manually (Kikinis, Zora)
   8. Re: GEANT4 & Slicer (Steve Pieper)
   9. Problem with jpeg, tif (????? ?????????)
  10. Re: Fwd: TCIA connection (Andrey Fedorov)
  11. Re: Fwd: TCIA connection (Felix)


----------------------------------------------------------------------

Message: 1
Date: Wed, 25 Jan 2017 17:02:14 +0000
From: Andrey Fedorov <[hidden email]>
To: F?lix Navarro Guirado <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Fwd: TCIA connection
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

For the IvyGAP collection, the issue appears to be with TCIA. It
returns empty image archive. I reported the problem to TCIA helpdesk.

For the Q&N Cetuximab, I am unable to reproduce the problem. Can you
try restarting Slicer and see whether the downloaded series shows up
in the database after restart? Sometime there are issues with
displaying data imported from the module. If this is not the case,
please provide more details to reproduce the problem
(subject/study/series).

Any particular reason you are using 4.6.2 and not the nightly version of Slicer?

On Wed, Jan 25, 2017 at 11:13 AM, Andrey Fedorov
<[hidden email]> wrote:
> Thank you for this detail - I can reproduce the problem with the
> IvyGap collection.
>
> On Wed, Jan 25, 2017 at 10:37 AM, F?lix Navarro Guirado
> <[hidden email]> wrote:
>>
>> I've re installed on slicer 4.6.2. Please take into account that the length
>> of total seems to have limit in Windows.
>>
>> This is the last update:
>>
>> I've tried to load on scene from IvyGAP. It seems to download images but
>> nothing is loaded (remember that I have a valid key) --> Log 1.
>> I've tried to store in my dicom database from H&N Cetuximab. Seems to
>> download but nothing appears in my dicom database. --> Log 2.
>>
>> -----------------------------------------------------------------------------------
>> ---------------------------- LOG 1
>> ------------------------------------------
>> -----------------------------------------------------------------------------------
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) - Switch to module:
>> "TCIABrowser"
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::generateQuery: query is: SELECT UID as UID,
>> PatientsName as Name, PatientsAge as Age, PatientsBirthDate as Date,
>> PatientID as "Subject ID" FROM Patients ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::updateQueries for Root: query is: SELECT UID as UID,
>> PatientsName as Name, PatientsAge as Age, PatientsBirthDate as Date,
>> PatientID as "Subject ID" FROM Patients ORDER BY "Name" DESC
>>
>> [WARNING][Qt] 25.01.2017 16:13:40 [] (unknown:0) - QSqlQuery::exec: database
>> not open
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::generateQuery: query is: SELECT UID as UID,
>> PatientsName as Name, PatientsAge as Age, PatientsBirthDate as Date,
>> PatientID as "Subject ID" FROM Patients ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::updateQueries for Root: query is: SELECT UID as UID,
>> PatientsName as Name, PatientsAge as Age, PatientsBirthDate as Date,
>> PatientID as "Subject ID" FROM Patients ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::generateQuery: query is: SELECT StudyInstanceUID as
>> UID, StudyDescription as Name, ModalitiesInStudy as Scan, StudyDate as Date,
>> AccessionNumber as Number, InstitutionName as Institution,
>> ReferringPhysician as Referrer, PerformingPhysiciansName as Performer FROM
>> Studies WHERE PatientsUID='33' ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::updateQueries for Patient: query is: SELECT
>> StudyInstanceUID as UID, StudyDescription as Name, ModalitiesInStudy as
>> Scan, StudyDate as Date, AccessionNumber as Number, InstitutionName as
>> Institution, ReferringPhysician as Referrer, PerformingPhysiciansName as
>> Performer FROM Studies WHERE PatientsUID='33' ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::generateQuery: query is: SELECT StudyInstanceUID as
>> UID, StudyDescription as Name, ModalitiesInStudy as Scan, StudyDate as Date,
>> AccessionNumber as Number, InstitutionName as Institution,
>> ReferringPhysician as Referrer, PerformingPhysiciansName as Performer FROM
>> Studies WHERE PatientsUID='30' ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::updateQueries for Patient: query is: SELECT
>> StudyInstanceUID as UID, StudyDescription as Name, ModalitiesInStudy as
>> Scan, StudyDate as Date, AccessionNumber as Number, InstitutionName as
>> Institution, ReferringPhysician as Referrer, PerformingPhysiciansName as
>> Performer FROM Studies WHERE PatientsUID='30' ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::generateQuery: query is: SELECT StudyInstanceUID as
>> UID, StudyDescription as Name, ModalitiesInStudy as Scan, StudyDate as Date,
>> AccessionNumber as Number, InstitutionName as Institution,
>> ReferringPhysician as Referrer, PerformingPhysiciansName as Performer FROM
>> Studies WHERE PatientsUID='31' ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::updateQueries for Patient: query is: SELECT
>> StudyInstanceUID as UID, StudyDescription as Name, ModalitiesInStudy as
>> Scan, StudyDate as Date, AccessionNumber as Number, InstitutionName as
>> Institution, ReferringPhysician as Referrer, PerformingPhysiciansName as
>> Performer FROM Studies WHERE PatientsUID='31' ORDER BY "Name" DESC
>>
>> [WARNING][Qt] 25.01.2017 16:14:30 [] (unknown:0) -
>> QSqlDatabasePrivate::addDatabase: duplicate connection name 'DICOM-DB', old
>> connection removed.
>>
>> [WARNING][Qt] 25.01.2017 16:14:30 [] (unknown:0) -
>> QSqlDatabasePrivate::addDatabase: duplicate connection name
>> 'DICOM-DBTagCache', old connection removed.
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - Traceback (most
>> recent call last):
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - File
>> "C:/Users/rayox010/AppData/Roaming/NA-MIC/Extensions-25516/TCIABrowser/lib/Slicer-4.6/qt-scripted-modules/TCIABrowser.py",
>> line 755, in onLoadButton
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) -
>> self.addSelectedToDownloadQueue()
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - File
>> "C:/Users/rayox010/AppData/Roaming/NA-MIC/Extensions-25516/TCIABrowser/lib/Slicer-4.6/qt-scripted-modules/TCIABrowser.py",
>> line 814, in addSelectedToDownloadQueue
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - loadables =
>> plugin.examine([fileList])
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - File
>> "C:\programas\Slicer_4_6_2\lib\Slicer-4.6\qt-scripted-modules\DICOMLib\DICOMPlugin.py",
>> line 119, in examine
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - return
>> self.examineForImport(fileList)
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - File
>> "C:/programas/Slicer_4_6_2/lib/Slicer-4.6/qt-scripted-modules/DICOMScalarVolumePlugin.py",
>> line 52, in examineForImport
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - loadablesForFiles =
>> self.examineFiles(files)
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - File
>> "C:/programas/Slicer_4_6_2/lib/Slicer-4.6/qt-scripted-modules/DICOMScalarVolumePlugin.py",
>> line 67, in examineFiles
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - seriesUID =
>> slicer.dicomDatabase.fileValue(files[0],self.tags['seriesUID'])
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - IndexError: tuple
>> index out of range
>>
>> [DEBUG][Qt] 25.01.2017 16:14:32 [] (unknown:0) - Could not load
>> "C:/programas/Slicer_4_6_2/XNATSlicer-master/XNATSlicer/Cache/downloads/data/experiments/xnat_E00074/scans/900/resources/1029/files/1.2.840.113564.99.1.71094327807604.8172.20169512715523.17674.2-900-1-9g8t6v.dcm"
>>
>> DCMTK says: No such file or directory
>>
>>
>>
>> -----------------------------------------------------------------------------------
>> ---------------------------- LOG 2
>> ------------------------------------------
>> -----------------------------------------------------------------------------------
>>
>> [DEBUG][Qt] 25.01.2017 16:21:55 [] (unknown:0) - Switch to module:
>> "TCIABrowser"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Processing
>> C:/Users/rayox010/Documents/SlicerDICOMDatabase/TCIALocal/7/images/1-091.dcm
>>
>> [WARNING][Qt] 25.01.2017 16:22:42 [] (unknown:0) - QSqlQuery::value: not
>> positioned on a valid record
>>
>> [WARNING][Qt] 25.01.2017 16:22:42 [] (unknown:0) - QSqlQuery::value: not
>> positioned on a valid record
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - inserting filePath:
>> "C:/Users/rayox010/Documents/SlicerDICOMDatabase/TCIALocal/7/images/1-091.dcm"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - database filename for
>> "1.3.6.1.4.1.14519.5.2.1.5099.8010.771104110219016637590309730419" is empty
>> - we should insert on top of it
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - This looks like a different
>> patient from last insert: "0522c0001"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - New patient inserted: 34
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - New patient inserted as :
>> 34
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Going to insert this
>> instance with dbPatientID: 34
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Need to insert new study:
>> "1.3.6.1.4.1.14519.5.2.1.5099.8010.256809878238026661650178294515"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Study Added
>>
>> [WARNING][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Statement: SELECT * FROM
>> Series WHERE SeriesInstanceUID = ?
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Need to insert new series:
>> "1.3.6.1.4.1.14519.5.2.1.5099.8010.293653169363509354643731389289"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Series Added
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Maybe add Instance
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Instance Added
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Processing
>> C:/Users/rayox010/Documents/SlicerDICOMDatabase/TCIALocal/7/images/10-100.dcm
>>
>> [WARNING][Qt] 25.01.2017 16:22:42 [] (unknown:0) - QSqlQuery::value: not
>> positioned on a valid record
>>
>> [WARNING][Qt] 25.01.2017 16:22:42 [] (unknown:0) - QSqlQuery::value: not
>> positioned on a valid record
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - inserting filePath:
>> "C:/Users/rayox010/Documents/SlicerDICOMDatabase/TCIALocal/7/images/10-100.dcm"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - database filename for
>> "1.3.6.1.4.1.14519.5.2.1.5099.8010.328644539230316634309847048059" is empty
>> - we should insert on top of it
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Going to insert this
>> instance with dbPatientID: 34
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Maybe add Instance
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Instance Added
>>
>> ......
>>
>> [DEBUG][Qt] 25.01.2017 16:22:50 [] (unknown:0) - Processing
>> C:/Users/rayox010/Documents/SlicerDICOMDatabase/TCIALocal/7/images/99-189.dcm
>>
>> [WARNING][Qt] 25.01.2017 16:22:50 [] (unknown:0) - QSqlQuery::value: not
>> positioned on a valid record
>>
>> [WARNING][Qt] 25.01.2017 16:22:50 [] (unknown:0) - QSqlQuery::value: not
>> positioned on a valid record
>>
>> [DEBUG][Qt] 25.01.2017 16:22:50 [] (unknown:0) - inserting filePath:
>> "C:/Users/rayox010/Documents/SlicerDICOMDatabase/TCIALocal/7/images/99-189.dcm"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:50 [] (unknown:0) - database filename for
>> "1.3.6.1.4.1.14519.5.2.1.5099.8010.317776145748140537057822982020" is empty
>> - we should insert on top of it
>>
>> [DEBUG][Qt] 25.01.2017 16:22:50 [] (unknown:0) - Going to insert this
>> instance with dbPatientID: 34
>>
>> [DEBUG][Qt] 25.01.2017 16:22:50 [] (unknown:0) - Maybe add Instance
>>
>> [DEBUG][Qt] 25.01.2017 16:22:50 [] (unknown:0) - Instance Added
>>
>>
>>
>> _______________________________________________
>> 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


------------------------------

Message: 2
Date: Wed, 25 Jan 2017 17:10:14 +0000
From: F?lix Navarro Guirado <[hidden email]>
To: Andrey Fedorov <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Fwd: TCIA connection
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

The patient appears in the DICOM database after restarting Slicer.

No, there is no reason. I just use to work with the last stable release of all programs when I use them in the hospital.

2017-01-25 18:02 GMT+01:00 Andrey Fedorov <[hidden email]<mailto:[hidden email]>>:
For the IvyGAP collection, the issue appears to be with TCIA. It
returns empty image archive. I reported the problem to TCIA helpdesk.

For the Q&N Cetuximab, I am unable to reproduce the problem. Can you
try restarting Slicer and see whether the downloaded series shows up
in the database after restart? Sometime there are issues with
displaying data imported from the module. If this is not the case,
please provide more details to reproduce the problem
(subject/study/series).

Any particular reason you are using 4.6.2 and not the nightly version of Slicer?

> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://massmail.spl.harvard.edu/public-archives/slicer-users/attachments/20170125/c933e5d5/attachment-0001.html>

------------------------------

Message: 3
Date: Wed, 25 Jan 2017 17:16:43 +0000
From: Andrey Fedorov <[hidden email]>
To: F?lix Navarro Guirado <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Fwd: TCIA connection
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

On Wed, Jan 25, 2017 at 12:10 PM, F?lix Navarro Guirado
<[hidden email]> wrote:
> The patient appears in the DICOM database after restarting Slicer.
>

Great, thanks. I've seen this issue sometime, but it is not reliably
reproducible...

> No, there is no reason. I just use to work with the last stable release of
> all programs when I use them in the hospital.
>

The designation of Slicer "stable" release is very misleading.
"Stable" is usually only relevant around the time it is released,
since most of the time important bugs and feature improvements are not
integrated back into the stable release. I recommend that you use
Nightly.

I've just committed updates to the code that improve logging and error
reporting, so that you have more information about what is going on
next time you have problems with the extension.

I will let you know when I hear from TCIA help desk about the IvyGAP
collection issue.


> 2017-01-25 18:02 GMT+01:00 Andrey Fedorov <[hidden email]>:
>>
>> For the IvyGAP collection, the issue appears to be with TCIA. It
>> returns empty image archive. I reported the problem to TCIA helpdesk.
>>
>> For the Q&N Cetuximab, I am unable to reproduce the problem. Can you
>> try restarting Slicer and see whether the downloaded series shows up
>> in the database after restart? Sometime there are issues with
>> displaying data imported from the module. If this is not the case,
>> please provide more details to reproduce the problem
>> (subject/study/series).
>>
>> Any particular reason you are using 4.6.2 and not the nightly version of
>> Slicer?
>>
>> > http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>


------------------------------

Message: 4
Date: Wed, 25 Jan 2017 17:27:08 +0000
From: Felix <[hidden email]>
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Extract Skull from MRI image
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Sorry, I forgot this thread.

I've just written to the author. I'll give you a feedback as soon as I have
an answer.

I meant a "homemade" module.



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Extract-Skull-from-MRI-image-tp4031404p4031658.html
Sent from the slicer-users mailing list archive at Nabble.com.


------------------------------

Message: 5
Date: Wed, 25 Jan 2017 22:02:02 +0000
From: Marlene Wigand <[hidden email]>
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] delete fibers manually
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hello everyone,

is there an option in Slicer 4 to delete fibers of a fiber tract manually? I remember that I was able to delete single fibers in Slicer 2.7 by moving the mouse over the fiber and pressing the d key but this is not working in Slicer 4.

I really appreciate your help!

Best, Marlene
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://massmail.spl.harvard.edu/public-archives/slicer-users/attachments/20170125/84bf4e6b/attachment-0001.html>

------------------------------

Message: 6
Date: Wed, 25 Jan 2017 22:28:41 +0000
From: Rutvij Kotecha <[hidden email]>
To: Marlene Wigand <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] delete fibers manually
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hi Marlene,

Can you please share a pic or two to explain your issue?

Thanks!

Rutvij

On Wed, Jan 25, 2017 at 2:02 PM, Marlene Wigand <[hidden email]<mailto:[hidden email]>> wrote:
Hello everyone,

is there an option in Slicer 4 to delete fibers of a fiber tract manually? I remember that I was able to delete single fibers in Slicer 2.7 by moving the mouse over the fiber and pressing the d key but this is not working in Slicer 4.

I really appreciate your help!

Best, Marlene

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://massmail.spl.harvard.edu/public-archives/slicer-users/attachments/20170125/404cdb1b/attachment-0001.html>

------------------------------

Message: 7
Date: Wed, 25 Jan 2017 22:37:22 +0000
From: "Kikinis, Zora" <[hidden email]>
To: Marlene Wigand <[hidden email]>, SPL Slicer Users
<[hidden email]>
Subject: Re: [slicer-users] delete fibers manually
Message-ID:
<[hidden email]>
Content-Type: text/plain; charset="windows-1252"

Marlena,

Go to Tractography Display,
Select the tract (displayed as tubes works best)
Open Fiber Bundle Selection
Enable Interactive Edit

in 3D viewer click on the tract to be deleted
Type d for delete

?Zora

From: slicer-users <[hidden email]<mailto:[hidden email]>> on behalf of Marlene Wigand <[hidden email]<mailto:[hidden email]>>
Date: Wednesday, January 25, 2017 at 5:02 PM
To: SPL Slicer Users <[hidden email]<mailto:[hidden email]>>
Subject: [slicer-users] delete fibers manually
Resent-From: <[hidden email]<mailto:[hidden email]>>
Resent-Date: Wednesday, January 25, 2017 at 5:03 PM

Hello everyone,

is there an option in Slicer 4 to delete fibers of a fiber tract manually? I remember that I was able to delete single fibers in Slicer 2.7 by moving the mouse over the fiber and pressing the d key but this is not working in Slicer 4.

I really appreciate your help!

Best, Marlene
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://massmail.spl.harvard.edu/public-archives/slicer-users/attachments/20170125/d0dca980/attachment-0001.html>

------------------------------

Message: 8
Date: Wed, 25 Jan 2017 23:32:09 +0000
From: Steve Pieper <[hidden email]>
To: Delvan Neville <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] GEANT4 & Slicer
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hi Delvan -

That sounds very cool, and from a quick look it seems the GEANT4 code is certainly powerful. Sometimes getting multiple python packages to work well together presents build issues, but I hope it would go smoothly.

Let us know if you run into any issues or questions.

Best,
Steve

On Tue, Jan 24, 2017 at 7:41 PM, Delvan Neville <[hidden email]<mailto:[hidden email]>> wrote:
Howdy all,

I'm working on an application so I can segment in Slicer, make surface meshes and use those to define the geometry for radiation transport in GEANT4. Since there is a Python wrapper for GEANT4 I believe I could build this as a publishable extension to Slicer rather than a separate executable that's able to read Slicer's output files. Anyone have an interest in this? If so, how would you plan to use it? (If there is interest such that I build it as an extension, I'd like to build it to be of use outside of our special use case, so knowing your intended use will help inform me on other features to either build in or leave me easy access in the structure of the code to build them in later).

FYI, I'll be using it for doing dose calculations for wildlife for environmental health physics, so features like calculating doses from a given concentration of a radionuclide in a given organ, specifying density & composition of tissues, or adding in planar or immersion external sources will be in already.

Sincerely,
Delvan Neville

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://massmail.spl.harvard.edu/public-archives/slicer-users/attachments/20170125/727f0b97/attachment-0001.html>

------------------------------

Message: 9
Date: Thu, 26 Jan 2017 14:48:48 +0000
From: ????? ????????? <[hidden email]>
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Problem with jpeg, tif
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="koi8-r"



Hello. I have a problem. 4.3, 4.6 and 4.7 version don`t want to load or process anyhow jpeg or tiff files or even nrrd, no reaction, some blink and nothing. I have sequence of microscopy images that I made with fotocamera (jpeg, tif). I tryed drag and drop, pushed Data button, File-Add Data, nothing worked. Of couse appear window "Add data into the scene" with my files, than Ok, after that short blink of download window and nothing - empty R,Y,G and Volume windows.
What I did wrong? What the source of images should be?
Thank you.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://massmail.spl.harvard.edu/public-archives/slicer-users/attachments/20170126/31938b95/attachment-0001.html>

------------------------------

Message: 10
Date: Thu, 26 Jan 2017 15:16:43 +0000
From: Andrey Fedorov <[hidden email]>
To: F?lix Navarro Guirado <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Fwd: TCIA connection
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

> I will let you know when I hear from TCIA help desk about the IvyGAP collection issue.

TCIA folks looked into the problem, and it seems to be resolved. I am
able to download datasets from the IvyGAP collection now.

On Wed, Jan 25, 2017 at 12:16 PM, Andrey Fedorov
<[hidden email]> wrote:
> On Wed, Jan 25, 2017 at 12:10 PM, F?lix Navarro Guirado
> <[hidden email]> wrote:
>> The patient appears in the DICOM database after restarting Slicer.
>>
>
> Great, thanks. I've seen this issue sometime, but it is not reliably
> reproducible...
>
>> No, there is no reason. I just use to work with the last stable release of
>> all programs when I use them in the hospital.
>>
>
> The designation of Slicer "stable" release is very misleading.
> "Stable" is usually only relevant around the time it is released,
> since most of the time important bugs and feature improvements are not
> integrated back into the stable release. I recommend that you use
> Nightly.
>
> I've just committed updates to the code that improve logging and error
> reporting, so that you have more information about what is going on
> next time you have problems with the extension.
>
> I will let you know when I hear from TCIA help desk about the IvyGAP
> collection issue.
>
>
>> 2017-01-25 18:02 GMT+01:00 Andrey Fedorov <[hidden email]>:
>>>
>>> For the IvyGAP collection, the issue appears to be with TCIA. It
>>> returns empty image archive. I reported the problem to TCIA helpdesk.
>>>
>>> For the Q&N Cetuximab, I am unable to reproduce the problem. Can you
>>> try restarting Slicer and see whether the downloaded series shows up
>>> in the database after restart? Sometime there are issues with
>>> displaying data imported from the module. If this is not the case,
>>> please provide more details to reproduce the problem
>>> (subject/study/series).
>>>
>>> Any particular reason you are using 4.6.2 and not the nightly version of
>>> Slicer?
>>>
>>> > 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


------------------------------

Message: 11
Date: Thu, 26 Jan 2017 15:28:14 +0000
From: Felix <[hidden email]>
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Fwd: TCIA connection
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

After the modification on the TCIA server Ivy GAP collection works for me.



--
View this message in context: http://slicer-users.65878.n3.nabble.com/TCIA-connection-tp4031550p4031665.html
Sent from the slicer-users mailing list archive at Nabble.com.


------------------------------

Subject: Digest Footer

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/admin/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject

------------------------------

End of slicer-users Digest, Vol 139, Issue 24
*********************************************



_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: slicer-users Digest

Andras Lasso-2

The mailing list server or your e-mail client could not handle Cyrillic letters in your name.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of ????? ?????????
Sent: January 26, 2017 12:19
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] slicer-users Digest

 

What does it meen this message? 
I am the 9th sender?



-------- Пересылаемое сообщение --------
От кого: [hidden email]
Кому: [hidden email]
Дата: Четверг, 26 января 2017, 19:00 +02:00
Тема: slicer-users Digest, Vol 139, Issue 24

Send slicer-users mailing list submissions to
[hidden email]

To subscribe or unsubscribe via the World Wide Web, visit
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
or, via email, send a message with subject or body 'help' to
[hidden email]

You can reach the person managing the list at
[hidden email]

When replying, please edit your Subject line so it is more specific
than "Re: Contents of slicer-users digest..."


Today's Topics:

   1. Re: Fwd: TCIA connection (Andrey Fedorov)
   2. Re: Fwd: TCIA connection (F?lix Navarro Guirado)
   3. Re: Fwd: TCIA connection (Andrey Fedorov)
   4. Re: Extract Skull from MRI image (Felix)
   5. delete fibers manually (Marlene Wigand)
   6. Re: delete fibers manually (Rutvij Kotecha)
   7. Re: delete fibers manually (Kikinis, Zora)
   8. Re: GEANT4 & Slicer (Steve Pieper)
   9. Problem with jpeg, tif (????? ?????????)
  10. Re: Fwd: TCIA connection (Andrey Fedorov)
  11. Re: Fwd: TCIA connection (Felix)


----------------------------------------------------------------------

Message: 1
Date: Wed, 25 Jan 2017 17:02:14 +0000
From: Andrey Fedorov <[hidden email]>
To: F?lix Navarro Guirado <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Fwd: TCIA connection
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

For the IvyGAP collection, the issue appears to be with TCIA. It
returns empty image archive. I reported the problem to TCIA helpdesk.

For the Q&N Cetuximab, I am unable to reproduce the problem. Can you
try restarting Slicer and see whether the downloaded series shows up
in the database after restart? Sometime there are issues with
displaying data imported from the module. If this is not the case,
please provide more details to reproduce the problem
(subject/study/series).

Any particular reason you are using 4.6.2 and not the nightly version of Slicer?

On Wed, Jan 25, 2017 at 11:13 AM, Andrey Fedorov
<[hidden email]> wrote:
> Thank you for this detail - I can reproduce the problem with the
> IvyGap collection.
>
> On Wed, Jan 25, 2017 at 10:37 AM, F?lix Navarro Guirado
> <[hidden email]> wrote:
>>
>> I've re installed on slicer 4.6.2. Please take into account that the length
>> of total seems to have limit in Windows.
>>
>> This is the last update:
>>
>> I've tried to load on scene from IvyGAP. It seems to download images but
>> nothing is loaded (remember that I have a valid key) --> Log 1.
>> I've tried to store in my dicom database from H&N Cetuximab. Seems to
>> download but nothing appears in my dicom database. --> Log 2.
>>
>> -----------------------------------------------------------------------------------
>> ---------------------------- LOG 1
>> ------------------------------------------
>> -----------------------------------------------------------------------------------
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) - Switch to module:
>> "TCIABrowser"
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::generateQuery: query is: SELECT UID as UID,
>> PatientsName as Name, PatientsAge as Age, PatientsBirthDate as Date,
>> PatientID as "Subject ID" FROM Patients ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::updateQueries for Root: query is: SELECT UID as UID,
>> PatientsName as Name, PatientsAge as Age, PatientsBirthDate as Date,
>> PatientID as "Subject ID" FROM Patients ORDER BY "Name" DESC
>>
>> [WARNING][Qt] 25.01.2017 16:13:40 [] (unknown:0) - QSqlQuery::exec: database
>> not open
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::generateQuery: query is: SELECT UID as UID,
>> PatientsName as Name, PatientsAge as Age, PatientsBirthDate as Date,
>> PatientID as "Subject ID" FROM Patients ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::updateQueries for Root: query is: SELECT UID as UID,
>> PatientsName as Name, PatientsAge as Age, PatientsBirthDate as Date,
>> PatientID as "Subject ID" FROM Patients ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::generateQuery: query is: SELECT StudyInstanceUID as
>> UID, StudyDescription as Name, ModalitiesInStudy as Scan, StudyDate as Date,
>> AccessionNumber as Number, InstitutionName as Institution,
>> ReferringPhysician as Referrer, PerformingPhysiciansName as Performer FROM
>> Studies WHERE PatientsUID='33' ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::updateQueries for Patient: query is: SELECT
>> StudyInstanceUID as UID, StudyDescription as Name, ModalitiesInStudy as
>> Scan, StudyDate as Date, AccessionNumber as Number, InstitutionName as
>> Institution, ReferringPhysician as Referrer, PerformingPhysiciansName as
>> Performer FROM Studies WHERE PatientsUID='33' ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::generateQuery: query is: SELECT StudyInstanceUID as
>> UID, StudyDescription as Name, ModalitiesInStudy as Scan, StudyDate as Date,
>> AccessionNumber as Number, InstitutionName as Institution,
>> ReferringPhysician as Referrer, PerformingPhysiciansName as Performer FROM
>> Studies WHERE PatientsUID='30' ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::updateQueries for Patient: query is: SELECT
>> StudyInstanceUID as UID, StudyDescription as Name, ModalitiesInStudy as
>> Scan, StudyDate as Date, AccessionNumber as Number, InstitutionName as
>> Institution, ReferringPhysician as Referrer, PerformingPhysiciansName as
>> Performer FROM Studies WHERE PatientsUID='30' ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::generateQuery: query is: SELECT StudyInstanceUID as
>> UID, StudyDescription as Name, ModalitiesInStudy as Scan, StudyDate as Date,
>> AccessionNumber as Number, InstitutionName as Institution,
>> ReferringPhysician as Referrer, PerformingPhysiciansName as Performer FROM
>> Studies WHERE PatientsUID='31' ORDER BY "Name" DESC
>>
>> [DEBUG][Qt] 25.01.2017 16:13:40 [] (unknown:0) -
>> ctkDICOMModelPrivate::updateQueries for Patient: query is: SELECT
>> StudyInstanceUID as UID, StudyDescription as Name, ModalitiesInStudy as
>> Scan, StudyDate as Date, AccessionNumber as Number, InstitutionName as
>> Institution, ReferringPhysician as Referrer, PerformingPhysiciansName as
>> Performer FROM Studies WHERE PatientsUID='31' ORDER BY "Name" DESC
>>
>> [WARNING][Qt] 25.01.2017 16:14:30 [] (unknown:0) -
>> QSqlDatabasePrivate::addDatabase: duplicate connection name 'DICOM-DB', old
>> connection removed.
>>
>> [WARNING][Qt] 25.01.2017 16:14:30 [] (unknown:0) -
>> QSqlDatabasePrivate::addDatabase: duplicate connection name
>> 'DICOM-DBTagCache', old connection removed.
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - Traceback (most
>> recent call last):
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - File
>> "C:/Users/rayox010/AppData/Roaming/NA-MIC/Extensions-25516/TCIABrowser/lib/Slicer-4.6/qt-scripted-modules/TCIABrowser.py",
>> line 755, in onLoadButton
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) -
>> self.addSelectedToDownloadQueue()
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - File
>> "C:/Users/rayox010/AppData/Roaming/NA-MIC/Extensions-25516/TCIABrowser/lib/Slicer-4.6/qt-scripted-modules/TCIABrowser.py",
>> line 814, in addSelectedToDownloadQueue
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - loadables =
>> plugin.examine([fileList])
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - File
>> "C:\programas\Slicer_4_6_2\lib\Slicer-4.6\qt-scripted-modules\DICOMLib\DICOMPlugin.py",
>> line 119, in examine
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - return
>> self.examineForImport(fileList)
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - File
>> "C:/programas/Slicer_4_6_2/lib/Slicer-4.6/qt-scripted-modules/DICOMScalarVolumePlugin.py",
>> line 52, in examineForImport
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - loadablesForFiles =
>> self.examineFiles(files)
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - File
>> "C:/programas/Slicer_4_6_2/lib/Slicer-4.6/qt-scripted-modules/DICOMScalarVolumePlugin.py",
>> line 67, in examineFiles
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - seriesUID =
>> slicer.dicomDatabase.fileValue(files[0],self.tags['seriesUID'])
>>
>> [CRITICAL][Stream] 25.01.2017 16:14:31 [] (unknown:0) - IndexError: tuple
>> index out of range
>>
>> [DEBUG][Qt] 25.01.2017 16:14:32 [] (unknown:0) - Could not load
>> "C:/programas/Slicer_4_6_2/XNATSlicer-master/XNATSlicer/Cache/downloads/data/experiments/xnat_E00074/scans/900/resources/1029/files/1.2.840.113564.99.1.71094327807604.8172.20169512715523.17674.2-900-1-9g8t6v.dcm"
>>
>> DCMTK says: No such file or directory
>>
>>
>>
>> -----------------------------------------------------------------------------------
>> ---------------------------- LOG 2
>> ------------------------------------------
>> -----------------------------------------------------------------------------------
>>
>> [DEBUG][Qt] 25.01.2017 16:21:55 [] (unknown:0) - Switch to module:
>> "TCIABrowser"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Processing
>> C:/Users/rayox010/Documents/SlicerDICOMDatabase/TCIALocal/7/images/1-091.dcm
>>
>> [WARNING][Qt] 25.01.2017 16:22:42 [] (unknown:0) - QSqlQuery::value: not
>> positioned on a valid record
>>
>> [WARNING][Qt] 25.01.2017 16:22:42 [] (unknown:0) - QSqlQuery::value: not
>> positioned on a valid record
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - inserting filePath:
>> "C:/Users/rayox010/Documents/SlicerDICOMDatabase/TCIALocal/7/images/1-091.dcm"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - database filename for
>> "1.3.6.1.4.1.14519.5.2.1.5099.8010.771104110219016637590309730419" is empty
>> - we should insert on top of it
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - This looks like a different
>> patient from last insert: "0522c0001"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - New patient inserted: 34
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - New patient inserted as :
>> 34
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Going to insert this
>> instance with dbPatientID: 34
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Need to insert new study:
>> "1.3.6.1.4.1.14519.5.2.1.5099.8010.256809878238026661650178294515"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Study Added
>>
>> [WARNING][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Statement: SELECT * FROM
>> Series WHERE SeriesInstanceUID = ?
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Need to insert new series:
>> "1.3.6.1.4.1.14519.5.2.1.5099.8010.293653169363509354643731389289"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Series Added
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Maybe add Instance
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Instance Added
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Processing
>> C:/Users/rayox010/Documents/SlicerDICOMDatabase/TCIALocal/7/images/10-100.dcm
>>
>> [WARNING][Qt] 25.01.2017 16:22:42 [] (unknown:0) - QSqlQuery::value: not
>> positioned on a valid record
>>
>> [WARNING][Qt] 25.01.2017 16:22:42 [] (unknown:0) - QSqlQuery::value: not
>> positioned on a valid record
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - inserting filePath:
>> "C:/Users/rayox010/Documents/SlicerDICOMDatabase/TCIALocal/7/images/10-100.dcm"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - database filename for
>> "1.3.6.1.4.1.14519.5.2.1.5099.8010.328644539230316634309847048059" is empty
>> - we should insert on top of it
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Going to insert this
>> instance with dbPatientID: 34
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Maybe add Instance
>>
>> [DEBUG][Qt] 25.01.2017 16:22:42 [] (unknown:0) - Instance Added
>>
>> ......
>>
>> [DEBUG][Qt] 25.01.2017 16:22:50 [] (unknown:0) - Processing
>> C:/Users/rayox010/Documents/SlicerDICOMDatabase/TCIALocal/7/images/99-189.dcm
>>
>> [WARNING][Qt] 25.01.2017 16:22:50 [] (unknown:0) - QSqlQuery::value: not
>> positioned on a valid record
>>
>> [WARNING][Qt] 25.01.2017 16:22:50 [] (unknown:0) - QSqlQuery::value: not
>> positioned on a valid record
>>
>> [DEBUG][Qt] 25.01.2017 16:22:50 [] (unknown:0) - inserting filePath:
>> "C:/Users/rayox010/Documents/SlicerDICOMDatabase/TCIALocal/7/images/99-189.dcm"
>>
>> [DEBUG][Qt] 25.01.2017 16:22:50 [] (unknown:0) - database filename for
>> "1.3.6.1.4.1.14519.5.2.1.5099.8010.317776145748140537057822982020" is empty
>> - we should insert on top of it
>>
>> [DEBUG][Qt] 25.01.2017 16:22:50 [] (unknown:0) - Going to insert this
>> instance with dbPatientID: 34
>>
>> [DEBUG][Qt] 25.01.2017 16:22:50 [] (unknown:0) - Maybe add Instance
>>
>> [DEBUG][Qt] 25.01.2017 16:22:50 [] (unknown:0) - Instance Added
>>
>>
>>
>> _______________________________________________
>> 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


------------------------------

Message: 2
Date: Wed, 25 Jan 2017 17:10:14 +0000
From: F?lix Navarro Guirado <[hidden email]>
To: Andrey Fedorov <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Fwd: TCIA connection
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

The patient appears in the DICOM database after restarting Slicer.

No, there is no reason. I just use to work with the last stable release of all programs when I use them in the hospital.

2017-01-25 18:02 GMT+01:00 Andrey Fedorov <[hidden email]<mailto:[hidden email]>>:
For the IvyGAP collection, the issue appears to be with TCIA. It
returns empty image archive. I reported the problem to TCIA helpdesk.

For the Q&N Cetuximab, I am unable to reproduce the problem. Can you
try restarting Slicer and see whether the downloaded series shows up
in the database after restart? Sometime there are issues with
displaying data imported from the module. If this is not the case,
please provide more details to reproduce the problem
(subject/study/series).

Any particular reason you are using 4.6.2 and not the nightly version of Slicer?

> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://massmail.spl.harvard.edu/public-archives/slicer-users/attachments/20170125/c933e5d5/attachment-0001.html>

------------------------------

Message: 3
Date: Wed, 25 Jan 2017 17:16:43 +0000
From: Andrey Fedorov <[hidden email]>
To: F?lix Navarro Guirado <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Fwd: TCIA connection
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

On Wed, Jan 25, 2017 at 12:10 PM, F?lix Navarro Guirado
<[hidden email]> wrote:
> The patient appears in the DICOM database after restarting Slicer.
>

Great, thanks. I've seen this issue sometime, but it is not reliably
reproducible...

> No, there is no reason. I just use to work with the last stable release of
> all programs when I use them in the hospital.
>

The designation of Slicer "stable" release is very misleading.
"Stable" is usually only relevant around the time it is released,
since most of the time important bugs and feature improvements are not
integrated back into the stable release. I recommend that you use
Nightly.

I've just committed updates to the code that improve logging and error
reporting, so that you have more information about what is going on
next time you have problems with the extension.

I will let you know when I hear from TCIA help desk about the IvyGAP
collection issue.


> 2017-01-25 18:02 GMT+01:00 Andrey Fedorov <[hidden email]>:
>>
>> For the IvyGAP collection, the issue appears to be with TCIA. It
>> returns empty image archive. I reported the problem to TCIA helpdesk.
>>
>> For the Q&N Cetuximab, I am unable to reproduce the problem. Can you
>> try restarting Slicer and see whether the downloaded series shows up
>> in the database after restart? Sometime there are issues with
>> displaying data imported from the module. If this is not the case,
>> please provide more details to reproduce the problem
>> (subject/study/series).
>>
>> Any particular reason you are using 4.6.2 and not the nightly version of
>> Slicer?
>>
>> > http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>


------------------------------

Message: 4
Date: Wed, 25 Jan 2017 17:27:08 +0000
From: Felix <[hidden email]>
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Extract Skull from MRI image
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Sorry, I forgot this thread.

I've just written to the author. I'll give you a feedback as soon as I have
an answer.

I meant a "homemade" module.



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Extract-Skull-from-MRI-image-tp4031404p4031658.html
Sent from the slicer-users mailing list archive at Nabble.com.


------------------------------

Message: 5
Date: Wed, 25 Jan 2017 22:02:02 +0000
From: Marlene Wigand <[hidden email]>
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] delete fibers manually
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hello everyone,

is there an option in Slicer 4 to delete fibers of a fiber tract manually? I remember that I was able to delete single fibers in Slicer 2.7 by moving the mouse over the fiber and pressing the d key but this is not working in Slicer 4.

I really appreciate your help!

Best, Marlene
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://massmail.spl.harvard.edu/public-archives/slicer-users/attachments/20170125/84bf4e6b/attachment-0001.html>

------------------------------

Message: 6
Date: Wed, 25 Jan 2017 22:28:41 +0000
From: Rutvij Kotecha <[hidden email]>
To: Marlene Wigand <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] delete fibers manually
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hi Marlene,

Can you please share a pic or two to explain your issue?

Thanks!

Rutvij

On Wed, Jan 25, 2017 at 2:02 PM, Marlene Wigand <[hidden email]<mailto:[hidden email]>> wrote:
Hello everyone,

is there an option in Slicer 4 to delete fibers of a fiber tract manually? I remember that I was able to delete single fibers in Slicer 2.7 by moving the mouse over the fiber and pressing the d key but this is not working in Slicer 4.

I really appreciate your help!

Best, Marlene

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://massmail.spl.harvard.edu/public-archives/slicer-users/attachments/20170125/404cdb1b/attachment-0001.html>

------------------------------

Message: 7
Date: Wed, 25 Jan 2017 22:37:22 +0000
From: "Kikinis, Zora" <[hidden email]>
To: Marlene Wigand <[hidden email]>, SPL Slicer Users
<[hidden email]>
Subject: Re: [slicer-users] delete fibers manually
Message-ID:
<[hidden email]>
Content-Type: text/plain; charset="windows-1252"

Marlena,

Go to Tractography Display,
Select the tract (displayed as tubes works best)
Open Fiber Bundle Selection
Enable Interactive Edit

in 3D viewer click on the tract to be deleted
Type d for delete

?Zora

From: slicer-users <[hidden email]<mailto:[hidden email]>> on behalf of Marlene Wigand <[hidden email]<mailto:[hidden email]>>
Date: Wednesday, January 25, 2017 at 5:02 PM
To: SPL Slicer Users <[hidden email]<mailto:[hidden email]>>
Subject: [slicer-users] delete fibers manually
Resent-From: <[hidden email]<mailto:[hidden email]>>
Resent-Date: Wednesday, January 25, 2017 at 5:03 PM

Hello everyone,

is there an option in Slicer 4 to delete fibers of a fiber tract manually? I remember that I was able to delete single fibers in Slicer 2.7 by moving the mouse over the fiber and pressing the d key but this is not working in Slicer 4.

I really appreciate your help!

Best, Marlene
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://massmail.spl.harvard.edu/public-archives/slicer-users/attachments/20170125/d0dca980/attachment-0001.html>

------------------------------

Message: 8
Date: Wed, 25 Jan 2017 23:32:09 +0000
From: Steve Pieper <[hidden email]>
To: Delvan Neville <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] GEANT4 & Slicer
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hi Delvan -

That sounds very cool, and from a quick look it seems the GEANT4 code is certainly powerful. Sometimes getting multiple python packages to work well together presents build issues, but I hope it would go smoothly.

Let us know if you run into any issues or questions.

Best,
Steve

On Tue, Jan 24, 2017 at 7:41 PM, Delvan Neville <[hidden email]<mailto:[hidden email]>> wrote:
Howdy all,

I'm working on an application so I can segment in Slicer, make surface meshes and use those to define the geometry for radiation transport in GEANT4. Since there is a Python wrapper for GEANT4 I believe I could build this as a publishable extension to Slicer rather than a separate executable that's able to read Slicer's output files. Anyone have an interest in this? If so, how would you plan to use it? (If there is interest such that I build it as an extension, I'd like to build it to be of use outside of our special use case, so knowing your intended use will help inform me on other features to either build in or leave me easy access in the structure of the code to build them in later).

FYI, I'll be using it for doing dose calculations for wildlife for environmental health physics, so features like calculating doses from a given concentration of a radionuclide in a given organ, specifying density & composition of tissues, or adding in planar or immersion external sources will be in already.

Sincerely,
Delvan Neville

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://massmail.spl.harvard.edu/public-archives/slicer-users/attachments/20170125/727f0b97/attachment-0001.html>

------------------------------

Message: 9
Date: Thu, 26 Jan 2017 14:48:48 +0000
From: ????? ????????? <[hidden email]>
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Problem with jpeg, tif
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="koi8-r"



Hello. I have a problem. 4.3, 4.6 and 4.7 version don`t want to load or process anyhow jpeg or tiff files or even nrrd, no reaction, some blink and nothing. I have sequence of microscopy images that I made with fotocamera (jpeg, tif). I tryed drag and drop, pushed Data button, File-Add Data, nothing worked. Of couse appear window "Add data into the scene" with my files, than Ok, after that short blink of download window and nothing - empty R,Y,G and Volume windows.
What I did wrong? What the source of images should be?
Thank you.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://massmail.spl.harvard.edu/public-archives/slicer-users/attachments/20170126/31938b95/attachment-0001.html>

------------------------------

Message: 10
Date: Thu, 26 Jan 2017 15:16:43 +0000
From: Andrey Fedorov <[hidden email]>
To: F?lix Navarro Guirado <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Fwd: TCIA connection
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

> I will let you know when I hear from TCIA help desk about the IvyGAP collection issue.

TCIA folks looked into the problem, and it seems to be resolved. I am
able to download datasets from the IvyGAP collection now.

On Wed, Jan 25, 2017 at 12:16 PM, Andrey Fedorov
<[hidden email]> wrote:
> On Wed, Jan 25, 2017 at 12:10 PM, F?lix Navarro Guirado
> <[hidden email]> wrote:
>> The patient appears in the DICOM database after restarting Slicer.
>>
>
> Great, thanks. I've seen this issue sometime, but it is not reliably
> reproducible...
>
>> No, there is no reason. I just use to work with the last stable release of
>> all programs when I use them in the hospital.
>>
>
> The designation of Slicer "stable" release is very misleading.
> "Stable" is usually only relevant around the time it is released,
> since most of the time important bugs and feature improvements are not
> integrated back into the stable release. I recommend that you use
> Nightly.
>
> I've just committed updates to the code that improve logging and error
> reporting, so that you have more information about what is going on
> next time you have problems with the extension.
>
> I will let you know when I hear from TCIA help desk about the IvyGAP
> collection issue.
>
>
>> 2017-01-25 18:02 GMT+01:00 Andrey Fedorov <[hidden email]>:
>>>
>>> For the IvyGAP collection, the issue appears to be with TCIA. It
>>> returns empty image archive. I reported the problem to TCIA helpdesk.
>>>
>>> For the Q&N Cetuximab, I am unable to reproduce the problem. Can you
>>> try restarting Slicer and see whether the downloaded series shows up
>>> in the database after restart? Sometime there are issues with
>>> displaying data imported from the module. If this is not the case,
>>> please provide more details to reproduce the problem
>>> (subject/study/series).
>>>
>>> Any particular reason you are using 4.6.2 and not the nightly version of
>>> Slicer?
>>>
>>> > 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


------------------------------

Message: 11
Date: Thu, 26 Jan 2017 15:28:14 +0000
From: Felix <[hidden email]>
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Fwd: TCIA connection
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

After the modification on the TCIA server Ivy GAP collection works for me.



--
View this message in context: http://slicer-users.65878.n3.nabble.com/TCIA-connection-tp4031550p4031665.html
Sent from the slicer-users mailing list archive at Nabble.com.


------------------------------

Subject: Digest Footer

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/admin/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject

------------------------------

End of slicer-users Digest, Vol 139, Issue 24
*********************************************

 



_______________________________________________
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