Re: volume format saving issues

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Re: volume format saving issues

Murat Maga

Apologies, here  are the missing screen captures

 

From: Murat Maga [mailto:[hidden email]]
Sent: Tuesday, September 08, 2015 11:25 PM
To: 'SPL Slicer Users' <[hidden email]>
Subject: volume format saving issues

 

Dear Slicer developers,

 

I strongly suggest that you consider making a default volume format a customization option in slicer. Here is a scenario that drives me crazy: We work extensively with  nii.gz format volumes that we use between Slicer and other image processing programs. If we modify any aspect of the volume property in slicer (say adjust voxel size, center etc), and need to save it Slicer does not keep the default format it read the input. If you are not careful it will save it as

 

Sample_data.nii.nrrd (1st screen shot)

 

I think this is a flawed behavior. It should not change the input format unless the user explicitly asks to do so, especially if it is a format it can save.

 

If you are careful and then change the output format to nii.gz then file name becomes

Sample_data.nii.nii.gz and this keeps going forever. (2nd screen shot)

 

This doubling the extension behavior happens for volume property files as well.

 

M


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Re: volume format saving issues

Andrey Fedorov-2
Murat, can you clarify - were these volumes modified after loading?

On Wed, Sep 9, 2015 at 2:26 AM, Murat Maga <[hidden email]> wrote:

> Apologies, here  are the missing screen captures
>
>
>
> From: Murat Maga [mailto:[hidden email]]
> Sent: Tuesday, September 08, 2015 11:25 PM
> To: 'SPL Slicer Users' <[hidden email]>
> Subject: volume format saving issues
>
>
>
> Dear Slicer developers,
>
>
>
> I strongly suggest that you consider making a default volume format a
> customization option in slicer. Here is a scenario that drives me crazy: We
> work extensively with  nii.gz format volumes that we use between Slicer and
> other image processing programs. If we modify any aspect of the volume
> property in slicer (say adjust voxel size, center etc), and need to save it
> Slicer does not keep the default format it read the input. If you are not
> careful it will save it as
>
>
>
> Sample_data.nii.nrrd (1st screen shot)
>
>
>
> I think this is a flawed behavior. It should not change the input format
> unless the user explicitly asks to do so, especially if it is a format it
> can save.
>
>
>
> If you are careful and then change the output format to nii.gz then file
> name becomes
>
> Sample_data.nii.nii.gz and this keeps going forever. (2nd screen shot)
>
>
>
> This doubling the extension behavior happens for volume property files as
> well.
>
>
>
> M
>
>
> _______________________________________________
> 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: volume format saving issues

Aucoin, Nicole
Hi Murat,

I made a lot of bug fixes[1] when working on the MRB/Scene Views bugs and
the file format issue was one that I know I worked on (as well as the
incorrect extension additions especially with the nii.gz format). Are you
still seeing this behaviour in the nightly build?

Nicole

[1] Integrated pull request with individual commits:
https://github.com/Slicer/Slicer/pull/288/commits (file extensions fixed
in the third commit)


On 9/9/15, 8:44 AM, "Andrey Fedorov" <[hidden email]> wrote:

>Murat, can you clarify - were these volumes modified after loading?
>
>On Wed, Sep 9, 2015 at 2:26 AM, Murat Maga <[hidden email]> wrote:
>> Apologies, here  are the missing screen captures
>>
>>
>>
>> From: Murat Maga [mailto:[hidden email]]
>> Sent: Tuesday, September 08, 2015 11:25 PM
>> To: 'SPL Slicer Users' <[hidden email]>
>> Subject: volume format saving issues
>>
>>
>>
>> Dear Slicer developers,
>>
>>
>>
>> I strongly suggest that you consider making a default volume format a
>> customization option in slicer. Here is a scenario that drives me
>>crazy: We
>> work extensively with  nii.gz format volumes that we use between Slicer
>>and
>> other image processing programs. If we modify any aspect of the volume
>> property in slicer (say adjust voxel size, center etc), and need to
>>save it
>> Slicer does not keep the default format it read the input. If you are
>>not
>> careful it will save it as
>>
>>
>>
>> Sample_data.nii.nrrd (1st screen shot)
>>
>>
>>
>> I think this is a flawed behavior. It should not change the input format
>> unless the user explicitly asks to do so, especially if it is a format
>>it
>> can save.
>>
>>
>>
>> If you are careful and then change the output format to nii.gz then file
>> name becomes
>>
>> Sample_data.nii.nii.gz and this keeps going forever. (2nd screen shot)
>>
>>
>>
>> This doubling the extension behavior happens for volume property files
>>as
>> well.
>>
>>
>>
>> M
>>
>>
>> _______________________________________________
>> 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

_______________________________________________
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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
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Re: volume format saving issues

Murat Maga
In reply to this post by Murat Maga
Yes, for example we adjust image spacing.
M

-----Original Message-----
From: Andrey Fedorov [mailto:[hidden email]]
Sent: Wednesday, September 09, 2015 5:44 AM
To: Murat Maga
Cc: SPL Slicer Users
Subject: Re: [slicer-users] volume format saving issues

Murat, can you clarify - were these volumes modified after loading?

On Wed, Sep 9, 2015 at 2:26 AM, Murat Maga <[hidden email]> wrote:

> Apologies, here  are the missing screen captures
>
>
>
> From: Murat Maga [mailto:[hidden email]]
> Sent: Tuesday, September 08, 2015 11:25 PM
> To: 'SPL Slicer Users' <[hidden email]>
> Subject: volume format saving issues
>
>
>
> Dear Slicer developers,
>
>
>
> I strongly suggest that you consider making a default volume format a
> customization option in slicer. Here is a scenario that drives me
> crazy: We work extensively with  nii.gz format volumes that we use
> between Slicer and other image processing programs. If we modify any
> aspect of the volume property in slicer (say adjust voxel size, center
> etc), and need to save it Slicer does not keep the default format it
> read the input. If you are not careful it will save it as
>
>
>
> Sample_data.nii.nrrd (1st screen shot)
>
>
>
> I think this is a flawed behavior. It should not change the input
> format unless the user explicitly asks to do so, especially if it is a
> format it can save.
>
>
>
> If you are careful and then change the output format to nii.gz then
> file name becomes
>
> Sample_data.nii.nii.gz and this keeps going forever. (2nd screen shot)
>
>
>
> This doubling the extension behavior happens for volume property files
> as well.
>
>
>
> M
>
>
> _______________________________________________
> 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
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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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Re: volume format saving issues

Murat Maga
In reply to this post by Andrey Fedorov-2
Hi Nicole,

I have not tried the latest nightly. We are working with a build from late
May (r24272).
M

-----Original Message-----
From: Aucoin, Nicole [mailto:[hidden email]]
Sent: Wednesday, September 09, 2015 7:21 AM
To: Andrey Fedorov; Murat Maga
Cc: SPL Slicer Users
Subject: Re: [slicer-users] volume format saving issues

Hi Murat,

I made a lot of bug fixes[1] when working on the MRB/Scene Views bugs and
the file format issue was one that I know I worked on (as well as the
incorrect extension additions especially with the nii.gz format). Are you
still seeing this behaviour in the nightly build?

Nicole

[1] Integrated pull request with individual commits:
https://github.com/Slicer/Slicer/pull/288/commits (file extensions fixed in
the third commit)


On 9/9/15, 8:44 AM, "Andrey Fedorov" <[hidden email]> wrote:

>Murat, can you clarify - were these volumes modified after loading?
>
>On Wed, Sep 9, 2015 at 2:26 AM, Murat Maga <[hidden email]> wrote:
>> Apologies, here  are the missing screen captures
>>
>>
>>
>> From: Murat Maga [mailto:[hidden email]]
>> Sent: Tuesday, September 08, 2015 11:25 PM
>> To: 'SPL Slicer Users' <[hidden email]>
>> Subject: volume format saving issues
>>
>>
>>
>> Dear Slicer developers,
>>
>>
>>
>> I strongly suggest that you consider making a default volume format a  
>>customization option in slicer. Here is a scenario that drives me
>>crazy: We
>> work extensively with  nii.gz format volumes that we use between
>>Slicer and  other image processing programs. If we modify any aspect
>>of the volume  property in slicer (say adjust voxel size, center etc),
>>and need to save it  Slicer does not keep the default format it read
>>the input. If you are not  careful it will save it as
>>
>>
>>
>> Sample_data.nii.nrrd (1st screen shot)
>>
>>
>>
>> I think this is a flawed behavior. It should not change the input
>>format  unless the user explicitly asks to do so, especially if it is
>>a format it  can save.
>>
>>
>>
>> If you are careful and then change the output format to nii.gz then
>> file name becomes
>>
>> Sample_data.nii.nii.gz and this keeps going forever. (2nd screen
>> shot)
>>
>>
>>
>> This doubling the extension behavior happens for volume property
>>files as  well.
>>
>>
>>
>> M
>>
>>
>> _______________________________________________
>> 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


_______________________________________________
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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Re: volume format saving issues

Aucoin, Nicole
In reply to this post by Andrey Fedorov-2
Hi Murat,

The changes I made are in as of svn 24399 so I think most if not all of
your issues should be fixed in the nightly.

Nicole

On 9/9/15, 3:19 PM, "Murat Maga" <[hidden email]> wrote:

>Hi Nicole,
>
>I have not tried the latest nightly. We are working with a build from late
>May (r24272).
>M
>
>-----Original Message-----
>From: Aucoin, Nicole [mailto:[hidden email]]
>Sent: Wednesday, September 09, 2015 7:21 AM
>To: Andrey Fedorov; Murat Maga
>Cc: SPL Slicer Users
>Subject: Re: [slicer-users] volume format saving issues
>
>Hi Murat,
>
>I made a lot of bug fixes[1] when working on the MRB/Scene Views bugs and
>the file format issue was one that I know I worked on (as well as the
>incorrect extension additions especially with the nii.gz format). Are you
>still seeing this behaviour in the nightly build?
>
>Nicole
>
>[1] Integrated pull request with individual commits:
>https://github.com/Slicer/Slicer/pull/288/commits (file extensions fixed
>in
>the third commit)
>
>
>On 9/9/15, 8:44 AM, "Andrey Fedorov" <[hidden email]> wrote:
>
>>Murat, can you clarify - were these volumes modified after loading?
>>
>>On Wed, Sep 9, 2015 at 2:26 AM, Murat Maga <[hidden email]> wrote:
>>> Apologies, here  are the missing screen captures
>>>
>>>
>>>
>>> From: Murat Maga [mailto:[hidden email]]
>>> Sent: Tuesday, September 08, 2015 11:25 PM
>>> To: 'SPL Slicer Users' <[hidden email]>
>>> Subject: volume format saving issues
>>>
>>>
>>>
>>> Dear Slicer developers,
>>>
>>>
>>>
>>> I strongly suggest that you consider making a default volume format a
>>>customization option in slicer. Here is a scenario that drives me
>>>crazy: We
>>> work extensively with  nii.gz format volumes that we use between
>>>Slicer and  other image processing programs. If we modify any aspect
>>>of the volume  property in slicer (say adjust voxel size, center etc),
>>>and need to save it  Slicer does not keep the default format it read
>>>the input. If you are not  careful it will save it as
>>>
>>>
>>>
>>> Sample_data.nii.nrrd (1st screen shot)
>>>
>>>
>>>
>>> I think this is a flawed behavior. It should not change the input
>>>format  unless the user explicitly asks to do so, especially if it is
>>>a format it  can save.
>>>
>>>
>>>
>>> If you are careful and then change the output format to nii.gz then
>>> file name becomes
>>>
>>> Sample_data.nii.nii.gz and this keeps going forever. (2nd screen
>>> shot)
>>>
>>>
>>>
>>> This doubling the extension behavior happens for volume property
>>>files as  well.
>>>
>>>
>>>
>>> M
>>>
>>>
>>> _______________________________________________
>>> 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
>
>

_______________________________________________
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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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