label statistics

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label statistics

Hassanzadeh, Elmira,M.D.

Hi all,

 

I have a problem with saving the .csv files of a set of previously created labels using label statistics module:

 

1.       The resulting csv file is empty

2.       However, I  don’t have any problem saving/reading csv files for newly created labels

3.       I have tried both stable and latest nightly build versions of slicer

4.       I am attaching one of the labels, corresponding csv file, and the error message

 

Thanks

Elmira

 


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error.png (77K) Download Attachment
label.nrrd (4K) Download Attachment
labelstat.csv Download Attachment
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Re: label statistics

Steve Pieper-2
Hi Elmira - 

I can see how this happens - it is related to a few changes in the label statistics module in the past year or so [1] having to do with mismatched geometry, possibly due to roundoff error (the resampled volume is no longer available when the csv is saved).  I'd need to see the grayscale you are using in order to really debug.

If you are sure you have the label map and the grayscale volume in the same geometry you could try using slicer 4.3.  

In the mean time it would be best to start a mantis issue on this - would you mind doing that?  I have some ideas about the best fix.

Thanks for reporting!
-Steve




On Mon, Jul 27, 2015 at 12:31 PM, Hassanzadeh, Elmira,M.D. <[hidden email]> wrote:

Hi all,

 

I have a problem with saving the .csv files of a set of previously created labels using label statistics module:

 

1.       The resulting csv file is empty

2.       However, I  don’t have any problem saving/reading csv files for newly created labels

3.       I have tried both stable and latest nightly build versions of slicer

4.       I am attaching one of the labels, corresponding csv file, and the error message

 

Thanks

Elmira

 


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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



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Re: label statistics

Andrey Fedorov-2
Steve,

Elmira demonstrated the problem to me today. The volumes are of
different geometry (segmentation done on a series different from the
greyscale volume used for statistics). The table is populated with the
results, it's just that the csv saving is broken.

AF

On Tue, Jul 28, 2015 at 11:58 AM, Steve Pieper <[hidden email]> wrote:

> Hi Elmira -
>
> I can see how this happens - it is related to a few changes in the label
> statistics module in the past year or so [1] having to do with mismatched
> geometry, possibly due to roundoff error (the resampled volume is no longer
> available when the csv is saved).  I'd need to see the grayscale you are
> using in order to really debug.
>
> If you are sure you have the label map and the grayscale volume in the same
> geometry you could try using slicer 4.3.
>
> In the mean time it would be best to start a mantis issue on this - would
> you mind doing that?  I have some ideas about the best fix.
>
> Thanks for reporting!
> -Steve
>
> [1]
> https://github.com/Slicer/Slicer/commits/master/Modules/Scripted/LabelStatistics/LabelStatistics.py
>
>
>
> On Mon, Jul 27, 2015 at 12:31 PM, Hassanzadeh, Elmira,M.D.
> <[hidden email]> wrote:
>>
>> Hi all,
>>
>>
>>
>> I have a problem with saving the .csv files of a set of previously created
>> labels using label statistics module:
>>
>>
>>
>> 1.       The resulting csv file is empty
>>
>> 2.       However, I  don’t have any problem saving/reading csv files for
>> newly created labels
>>
>> 3.       I have tried both stable and latest nightly build versions of
>> slicer
>>
>> 4.       I am attaching one of the labels, corresponding csv file, and the
>> error message
>>
>>
>>
>> Thanks
>>
>> Elmira
>>
>>
>>
>>
>> _______________________________________________
>> 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
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>
>
> _______________________________________________
> 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
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: label statistics

Hassanzadeh, Elmira,M.D.
In reply to this post by Hassanzadeh, Elmira,M.D.

Hi Steve,

 

Thank you for your email. Well the sequence used for labeling was T2W but  the greyscale that I am trying to get label statistics on is ADC. so as they have quite different geometry, maybe this is the reason. But wouldn’t that be better if we could get the results regardless of the difference in geometry? Because for some projects the difference is insignificant.

If you think we still need to start a mantis issue, I would be happy to do that, but I have never heard of it and don’t know the steps.

I can follow your lead.

 

Thanks

Elmira

 

 

From: Steve Pieper [mailto:[hidden email]]
Sent: Tuesday, July 28, 2015 11:58 AM
To: Hassanzadeh, Elmira,M.D.
Cc: SPL Slicer Users
Subject: Re: [slicer-users] label statistics

 

Hi Elmira - 

 

I can see how this happens - it is related to a few changes in the label statistics module in the past year or so [1] having to do with mismatched geometry, possibly due to roundoff error (the resampled volume is no longer available when the csv is saved).  I'd need to see the grayscale you are using in order to really debug.

 

If you are sure you have the label map and the grayscale volume in the same geometry you could try using slicer 4.3.  

 

In the mean time it would be best to start a mantis issue on this - would you mind doing that?  I have some ideas about the best fix.

 

Thanks for reporting!

-Steve

 

 

 

 

On Mon, Jul 27, 2015 at 12:31 PM, Hassanzadeh, Elmira,M.D. <[hidden email]> wrote:

Hi all,

 

I have a problem with saving the .csv files of a set of previously created labels using label statistics module:

 

1.       The resulting csv file is empty

2.       However, I  don’t have any problem saving/reading csv files for newly created labels

3.       I have tried both stable and latest nightly build versions of slicer

4.       I am attaching one of the labels, corresponding csv file, and the error message

 

Thanks

Elmira

 


_______________________________________________
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[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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 


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Re: label statistics

Steve Pieper-2
In reply to this post by Steve Pieper-2
Right Andrey - the issue is in the saving.  When the label has different geometry it is resampled [1] and passed to the logic.  But then it's removed from the scene [2].  This means there will be no display node when it tries to write the csv file.

I think a better solution is to populate the color name in the logic.labelStats with the other items so we don't need to access the labelNode at all when saving the csv.


On Tue, Jul 28, 2015 at 12:32 PM, Andrey Fedorov <[hidden email]> wrote:
Steve,

Elmira demonstrated the problem to me today. The volumes are of
different geometry (segmentation done on a series different from the
greyscale volume used for statistics). The table is populated with the
results, it's just that the csv saving is broken.

AF

On Tue, Jul 28, 2015 at 11:58 AM, Steve Pieper <[hidden email]> wrote:
> Hi Elmira -
>
> I can see how this happens - it is related to a few changes in the label
> statistics module in the past year or so [1] having to do with mismatched
> geometry, possibly due to roundoff error (the resampled volume is no longer
> available when the csv is saved).  I'd need to see the grayscale you are
> using in order to really debug.
>
> If you are sure you have the label map and the grayscale volume in the same
> geometry you could try using slicer 4.3.
>
> In the mean time it would be best to start a mantis issue on this - would
> you mind doing that?  I have some ideas about the best fix.
>
> Thanks for reporting!
> -Steve
>
> [1]
> https://github.com/Slicer/Slicer/commits/master/Modules/Scripted/LabelStatistics/LabelStatistics.py
>
>
>
> On Mon, Jul 27, 2015 at 12:31 PM, Hassanzadeh, Elmira,M.D.
> <[hidden email]> wrote:
>>
>> Hi all,
>>
>>
>>
>> I have a problem with saving the .csv files of a set of previously created
>> labels using label statistics module:
>>
>>
>>
>> 1.       The resulting csv file is empty
>>
>> 2.       However, I  don’t have any problem saving/reading csv files for
>> newly created labels
>>
>> 3.       I have tried both stable and latest nightly build versions of
>> slicer
>>
>> 4.       I am attaching one of the labels, corresponding csv file, and the
>> error message
>>
>>
>>
>> Thanks
>>
>> Elmira
>>
>>
>>
>>
>> _______________________________________________
>> 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
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>
>
> _______________________________________________
> 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
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>


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Re: label statistics

Steve Pieper-2
In reply to this post by Hassanzadeh, Elmira,M.D.
Hi Elmira - 

Yes, we want to use the resampled data for accurate calculations.

The process is described on this page:

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Report_a_problem

Basically just paste in the contents of the email and then we can use mantis to track the state.

Thanks again,
-Steve

On Tue, Jul 28, 2015 at 12:33 PM, Hassanzadeh, Elmira,M.D. <[hidden email]> wrote:

Hi Steve,

 

Thank you for your email. Well the sequence used for labeling was T2W but  the greyscale that I am trying to get label statistics on is ADC. so as they have quite different geometry, maybe this is the reason. But wouldn’t that be better if we could get the results regardless of the difference in geometry? Because for some projects the difference is insignificant.

If you think we still need to start a mantis issue, I would be happy to do that, but I have never heard of it and don’t know the steps.

I can follow your lead.

 

Thanks

Elmira

 

 

From: Steve Pieper [mailto:[hidden email]]
Sent: Tuesday, July 28, 2015 11:58 AM
To: Hassanzadeh, Elmira,M.D.
Cc: SPL Slicer Users
Subject: Re: [slicer-users] label statistics

 

Hi Elmira - 

 

I can see how this happens - it is related to a few changes in the label statistics module in the past year or so [1] having to do with mismatched geometry, possibly due to roundoff error (the resampled volume is no longer available when the csv is saved).  I'd need to see the grayscale you are using in order to really debug.

 

If you are sure you have the label map and the grayscale volume in the same geometry you could try using slicer 4.3.  

 

In the mean time it would be best to start a mantis issue on this - would you mind doing that?  I have some ideas about the best fix.

 

Thanks for reporting!

-Steve

 

 

 

 

On Mon, Jul 27, 2015 at 12:31 PM, Hassanzadeh, Elmira,M.D. <[hidden email]> wrote:

Hi all,

 

I have a problem with saving the .csv files of a set of previously created labels using label statistics module:

 

1.       The resulting csv file is empty

2.       However, I  don’t have any problem saving/reading csv files for newly created labels

3.       I have tried both stable and latest nightly build versions of slicer

4.       I am attaching one of the labels, corresponding csv file, and the error message

 

Thanks

Elmira

 


_______________________________________________
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
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 



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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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dispose of the e-mail.