MultiVolume Explorer

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MultiVolume Explorer

Nassir Al-Khishman

Hello,


I have a dynamic MRI slice from which I want to extract a signal intensity graph over time. 

On the multivolume explorer module, interactive charting works for the probe, but when I create a label map and then click chart, I just get blank white square(no grid).

I've tried the module's sample dynamic prostate data, and that charted fine for me. Because that worked, I used matlab to locate the frames of a single slice from that sample data, and copy the header information onto my slices. Still get the same blank white square(no grid)


Thanks,

Nas


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Re: MultiVolume Explorer

Andrey Fedorov-2
On Thu, Aug 4, 2016 at 10:53 AM, Nassir Al-Khishman <[hidden email]> wrote:
> On the multivolume explorer module, interactive charting works for the
> probe, but when I create a label map and then click chart, I just get blank
> white square(no grid).
>

Can you describe the process of how you create the label map?

You first need to create a copy of one frame from the dynamic sequence
(by checking "Enable copying"), and then create segmentation on that
frame.

> I've tried the module's sample dynamic prostate data, and that charted fine
> for me. Because that worked, I used matlab to locate the frames of a single
> slice from that sample data, and copy the header information onto my slices.
> Still get the same blank white square(no grid).
>
>
> Thanks,
>
> Nas
>
>
> _______________________________________________
> 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: MultiVolume Explorer

Steve Pieper-2

On Thu, Aug 4, 2016 at 11:47 AM, Andrey Fedorov <[hidden email]> wrote:
On Thu, Aug 4, 2016 at 10:53 AM, Nassir Al-Khishman <[hidden email]> wrote:
> On the multivolume explorer module, interactive charting works for the
> probe, but when I create a label map and then click chart, I just get blank
> white square(no grid).
>

Can you describe the process of how you create the label map?

You first need to create a copy of one frame from the dynamic sequence
(by checking "Enable copying"), and then create segmentation on that
frame.

> I've tried the module's sample dynamic prostate data, and that charted fine
> for me. Because that worked, I used matlab to locate the frames of a single
> slice from that sample data, and copy the header information onto my slices.
> Still get the same blank white square(no grid).
>
>
> Thanks,
>
> Nas
>
>
> _______________________________________________
> 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: MultiVolume Explorer

Nassir Al-Khishman
In reply to this post by Andrey Fedorov-2

Hello again,

Yeah! I attempted to make a label through the frame copy function.


The error log says that something like" Point 68,53,-1 [sometimes with different X,Y,Z coordinates] is not in valid Extent P1(0,0,0) and P2(127,127,0)." My slice is all on the Z=0 plane and is 127*127 across. I thought maybe I'd try making other labels, each in a plane of their own(Z=1 and Z=-1). When I try to chart those now I get no error in the log. It's probably worthwhile noting that I am able to extract values from the Label statistics module! (just not dynamic)


Thanks again


From: Steve Pieper <[hidden email]>
Sent: August 4, 2016 3:12:05 PM
To: Andrey Fedorov
Cc: Nassir Al-Khishman; SPL Slicer Users
Subject: Re: [slicer-users] MultiVolume Explorer
 

On Thu, Aug 4, 2016 at 11:47 AM, Andrey Fedorov <[hidden email]> wrote:
On Thu, Aug 4, 2016 at 10:53 AM, Nassir Al-Khishman <[hidden email]> wrote:
> On the multivolume explorer module, interactive charting works for the
> probe, but when I create a label map and then click chart, I just get blank
> white square(no grid).
>

Can you describe the process of how you create the label map?

You first need to create a copy of one frame from the dynamic sequence
(by checking "Enable copying"), and then create segmentation on that
frame.

> I've tried the module's sample dynamic prostate data, and that charted fine
> for me. Because that worked, I used matlab to locate the frames of a single
> slice from that sample data, and copy the header information onto my slices.
> Still get the same blank white square(no grid).
>
>
> Thanks,
>
> Nas
>
>
> _______________________________________________
> 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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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: MultiVolume Explorer

Andrey Fedorov-2
In reply to this post by Andrey Fedorov-2
It is not easy to debug this remotely.

Would you be able to share a de-identified version of the data so I
could take a look?

On Fri, Aug 5, 2016 at 10:58 AM, Nassir Al-Khishman <[hidden email]> wrote:

> Hello again,
>
> Yeah! I attempted to make a label through the frame copy function.
>
>
> The error log says that something like" Point 68,53,-1 [sometimes with
> different X,Y,Z coordinates] is not in valid Extent P1(0,0,0) and
> P2(127,127,0)." My slice is all on the Z=0 plane and is 127*127 across. I
> thought maybe I'd try making other labels, each in a plane of their own(Z=1
> and Z=-1). When I try to chart those now I get no error in the log. It's
> probably worthwhile noting that I am able to extract values from the Label
> statistics module! (just not dynamic)
>
>
> Thanks again
>
> ________________________________
> From: Steve Pieper <[hidden email]>
> Sent: August 4, 2016 3:12:05 PM
> To: Andrey Fedorov
> Cc: Nassir Al-Khishman; SPL Slicer Users
> Subject: Re: [slicer-users] MultiVolume Explorer
>
> Also you should have a look in the error log.
>
> https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/ErrorLog
>
> On Thu, Aug 4, 2016 at 11:47 AM, Andrey Fedorov <[hidden email]>
> wrote:
>>
>> On Thu, Aug 4, 2016 at 10:53 AM, Nassir Al-Khishman <[hidden email]>
>> wrote:
>> > On the multivolume explorer module, interactive charting works for the
>> > probe, but when I create a label map and then click chart, I just get
>> > blank
>> > white square(no grid).
>> >
>>
>> Can you describe the process of how you create the label map?
>>
>> You first need to create a copy of one frame from the dynamic sequence
>> (by checking "Enable copying"), and then create segmentation on that
>> frame.
>>
>> > I've tried the module's sample dynamic prostate data, and that charted
>> > fine
>> > for me. Because that worked, I used matlab to locate the frames of a
>> > single
>> > slice from that sample data, and copy the header information onto my
>> > slices.
>> > Still get the same blank white square(no grid).
>> >
>> >
>> > Thanks,
>> >
>> > Nas
>> >
>> >
>> > _______________________________________________
>> > 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: MultiVolume Explorer

Andrey Fedorov-2
To close this issue, it was debugged and resolved via off-the-list
communication.

The issue in MultiVolumeImporter (off-by-one) was fixed, and the
change in hash has been committed to the Slicer source.

On Fri, Aug 5, 2016 at 11:00 AM, Andrey Fedorov
<[hidden email]> wrote:

> It is not easy to debug this remotely.
>
> Would you be able to share a de-identified version of the data so I
> could take a look?
>
> On Fri, Aug 5, 2016 at 10:58 AM, Nassir Al-Khishman <[hidden email]> wrote:
>> Hello again,
>>
>> Yeah! I attempted to make a label through the frame copy function.
>>
>>
>> The error log says that something like" Point 68,53,-1 [sometimes with
>> different X,Y,Z coordinates] is not in valid Extent P1(0,0,0) and
>> P2(127,127,0)." My slice is all on the Z=0 plane and is 127*127 across. I
>> thought maybe I'd try making other labels, each in a plane of their own(Z=1
>> and Z=-1). When I try to chart those now I get no error in the log. It's
>> probably worthwhile noting that I am able to extract values from the Label
>> statistics module! (just not dynamic)
>>
>>
>> Thanks again
>>
>> ________________________________
>> From: Steve Pieper <[hidden email]>
>> Sent: August 4, 2016 3:12:05 PM
>> To: Andrey Fedorov
>> Cc: Nassir Al-Khishman; SPL Slicer Users
>> Subject: Re: [slicer-users] MultiVolume Explorer
>>
>> Also you should have a look in the error log.
>>
>> https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/ErrorLog
>>
>> On Thu, Aug 4, 2016 at 11:47 AM, Andrey Fedorov <[hidden email]>
>> wrote:
>>>
>>> On Thu, Aug 4, 2016 at 10:53 AM, Nassir Al-Khishman <[hidden email]>
>>> wrote:
>>> > On the multivolume explorer module, interactive charting works for the
>>> > probe, but when I create a label map and then click chart, I just get
>>> > blank
>>> > white square(no grid).
>>> >
>>>
>>> Can you describe the process of how you create the label map?
>>>
>>> You first need to create a copy of one frame from the dynamic sequence
>>> (by checking "Enable copying"), and then create segmentation on that
>>> frame.
>>>
>>> > I've tried the module's sample dynamic prostate data, and that charted
>>> > fine
>>> > for me. Because that worked, I used matlab to locate the frames of a
>>> > single
>>> > slice from that sample data, and copy the header information onto my
>>> > slices.
>>> > Still get the same blank white square(no grid).
>>> >
>>> >
>>> > Thanks,
>>> >
>>> > Nas
>>> >
>>> >
>>> > _______________________________________________
>>> > 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
>>
>>
> _______________________________________________
> 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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