Opacity of models/slices intersection

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

Opacity of models/slices intersection

Fernando Pérez-García
Hi all,

I just noticed that when one changes the opacity of a model, the opacity of
its slice intersection is also modified. I think this new behavior is
interesting, but not always desired. I can't find the commit that changed
this.

Is there a way to link/unlink 2D and 3D opacity? As in the Segmentations
module, where one has a lot of control about opacities.

Best,
Fernando



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Opacity-of-models-slices-intersection-tp4031685.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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: Opacity of models/slices intersection

Andras Lasso-2
Thank you for reporting this. The modification was introduced when support for volumetric mesh visualization was added recently.

For now, I've restored the original behavior (keep slice intersections 100% opaque, apply display node's opacity to 3D views only). If opaque slice intersection is not suitable for visualization of volumetric meshes then a new attribute (SliceIntersectionOpacity) should be added.

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Fernando Pérez-García
Sent: January 30, 2017 12:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Opacity of models/slices intersection

Hi all,

I just noticed that when one changes the opacity of a model, the opacity of its slice intersection is also modified. I think this new behavior is interesting, but not always desired. I can't find the commit that changed this.

Is there a way to link/unlink 2D and 3D opacity? As in the Segmentations module, where one has a lot of control about opacities.

Best,
Fernando



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Opacity-of-models-slices-intersection-tp4031685.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Opacity of models/slices intersection

Fernando Pérez-García
In reply to this post by Fernando Pérez-García
Hi Andras,

Thank you. I think it would be good to be able to modify them independently with SliceIntersectionOpacity.


Fernando

2017-01-31 4:03 GMT+01:00 Andras Lasso <[hidden email]>:
Thank you for reporting this. The modification was introduced when support for volumetric mesh visualization was added recently.

For now, I've restored the original behavior (keep slice intersections 100% opaque, apply display node's opacity to 3D views only). If opaque slice intersection is not suitable for visualization of volumetric meshes then a new attribute (SliceIntersectionOpacity) should be added.

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Fernando Pérez-García
Sent: January 30, 2017 12:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Opacity of models/slices intersection

Hi all,

I just noticed that when one changes the opacity of a model, the opacity of its slice intersection is also modified. I think this new behavior is interesting, but not always desired. I can't find the commit that changed this.

Is there a way to link/unlink 2D and 3D opacity? As in the Segmentations module, where one has a lot of control about opacities.

Best,
Fernando



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Opacity-of-models-slices-intersection-tp4031685.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

DICOM patcher Module

Lars Grant-West
In reply to this post by Andras Lasso-2
I’ve been experimenting with running the DICOM Patcher module on a folder full of DICOM slices, but am finding that the module is stripping out the sequential file numbering, and puts each image into it’s own individual nest of folders, three deep.

As a result, image J (Fiji) won’t see the images to process them, photoshop can’t batch rename them, and I can’t seem to get them to import into 3D slicer as anything 

Original file directory:

Resulting file directory after running DICOM Patcher

Result when I attempt to import resulting folder

Is there a way to get the patcher to leave the image files in a single directory un-nested and sequentially named? 


I’ve tried unchecking the different parameters, but unless the three shown below are checked, I get an error.


I’m still doing this in an attempt to standardize the value range in the slices so I don’t get this kind of banding.


Thanks,

Lars




On Jan 30, 2017, at 10:03 PM, Andras Lasso <[hidden email]> wrote:

Thank you for reporting this. The modification was introduced when support for volumetric mesh visualization was added recently.

For now, I've restored the original behavior (keep slice intersections 100% opaque, apply display node's opacity to 3D views only). If opaque slice intersection is not suitable for visualization of volumetric meshes then a new attribute (SliceIntersectionOpacity) should be added.

Andras

-----Original Message-----
From: slicer-users [[hidden email]] On Behalf Of Fernando Pérez-García
Sent: January 30, 2017 12:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Opacity of models/slices intersection

Hi all,

I just noticed that when one changes the opacity of a model, the opacity of its slice intersection is also modified. I think this new behavior is interesting, but not always desired. I can't find the commit that changed this.

Is there a way to link/unlink 2D and 3D opacity? As in the Segmentations module, where one has a lot of control about opacities.

Best,
Fernando



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Opacity-of-models-slices-intersection-tp4031685.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: DICOM patcher Module

Steve Pieper-2
Hi Lars -

Odd that each slice appears to have a different patient ID.  Certainly that's not normal DICOM.

Here's a utility that might help - it allows you to create an arbitrary directory/filename convention based on any of the dicom tags:

https://github.com/pieper/dicomsort

HTH,
Steve

On Wed, Feb 1, 2017 at 9:10 AM, Lars Grant-West <[hidden email]> wrote:
I’ve been experimenting with running the DICOM Patcher module on a folder full of DICOM slices, but am finding that the module is stripping out the sequential file numbering, and puts each image into it’s own individual nest of folders, three deep.

As a result, image J (Fiji) won’t see the images to process them, photoshop can’t batch rename them, and I can’t seem to get them to import into 3D slicer as anything 

Original file directory:

Resulting file directory after running DICOM Patcher

Result when I attempt to import resulting folder

Is there a way to get the patcher to leave the image files in a single directory un-nested and sequentially named? 


I’ve tried unchecking the different parameters, but unless the three shown below are checked, I get an error.


I’m still doing this in an attempt to standardize the value range in the slices so I don’t get this kind of banding.


Thanks,

Lars




On Jan 30, 2017, at 10:03 PM, Andras Lasso <[hidden email]> wrote:

Thank you for reporting this. The modification was introduced when support for volumetric mesh visualization was added recently.

For now, I've restored the original behavior (keep slice intersections 100% opaque, apply display node's opacity to 3D views only). If opaque slice intersection is not suitable for visualization of volumetric meshes then a new attribute (SliceIntersectionOpacity) should be added.

Andras

-----Original Message-----
From: slicer-users [[hidden email]] On Behalf Of Fernando Pérez-García
Sent: January 30, 2017 12:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Opacity of models/slices intersection

Hi all,

I just noticed that when one changes the opacity of a model, the opacity of its slice intersection is also modified. I think this new behavior is interesting, but not always desired. I can't find the commit that changed this.

Is there a way to link/unlink 2D and 3D opacity? As in the Segmentations module, where one has a lot of control about opacities.

Best,
Fernando



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Opacity-of-models-slices-intersection-tp4031685.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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


_______________________________________________
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: DICOM patcher Module

Lars Grant-West
In reply to this post by Lars Grant-West
I’ve found a lot of the files on Morphosource seem to be labeled this way.

Holy cow. That looks great…but after downloading, signing up for Github and looking around it looks like I’d have to code code to get this working. This is well beyond my current capabilities

I’ll have to look for a batch processor that will be able to do the legwork of pulling this out.

Thank you though. I appreciate the help.

Lars


On Feb 1, 2017, at 9:28 AM, Steve Pieper <[hidden email]> wrote: 

Hi Lars -

Odd that each slice appears to have a different patient ID.  Certainly that's not normal DICOM.

Here's a utility that might help - it allows you to create an arbitrary directory/filename convention based on any of the dicom tags:

https://github.com/pieper/dicomsort

HTH,
Steve

On Wed, Feb 1, 2017 at 9:10 AM, Lars Grant-West <[hidden email]> wrote:
I’ve been experimenting with running the DICOM Patcher module on a folder full of DICOM slices, but am finding that the module is stripping out the sequential file numbering, and puts each image into it’s own individual nest of folders, three deep.

As a result, image J (Fiji) won’t see the images to process them, photoshop can’t batch rename them, and I can’t seem to get them to import into 3D slicer as anything 

Original file directory:
<Screen Shot 2017-02-01 at 8.51.14 AM.png>

Resulting file directory after running DICOM Patcher
<Screen Shot 2017-02-01 at 8.51.07 AM.png>

Result when I attempt to import resulting folder
<Screen Shot 2017-02-01 at 8.55.53 AM.png>

Is there a way to get the patcher to leave the image files in a single directory un-nested and sequentially named? 


I’ve tried unchecking the different parameters, but unless the three shown below are checked, I get an error.

<Screen Shot 2017-02-01 at 9.03.00 AM.png>

I’m still doing this in an attempt to standardize the value range in the slices so I don’t get this kind of banding.

<Screen-Shot-2017-02-01-at-9.08.57-AM.jpg>

Thanks,

Lars




On Jan 30, 2017, at 10:03 PM, Andras Lasso <[hidden email]> wrote:

Thank you for reporting this. The modification was introduced when support for volumetric mesh visualization was added recently.

For now, I've restored the original behavior (keep slice intersections 100% opaque, apply display node's opacity to 3D views only). If opaque slice intersection is not suitable for visualization of volumetric meshes then a new attribute (SliceIntersectionOpacity) should be added.

Andras

-----Original Message-----
From: slicer-users [[hidden email]] On Behalf Of Fernando Pérez-García
Sent: January 30, 2017 12:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Opacity of models/slices intersection

Hi all,

I just noticed that when one changes the opacity of a model, the opacity of its slice intersection is also modified. I think this new behavior is interesting, but not always desired. I can't find the commit that changed this.

Is there a way to link/unlink 2D and 3D opacity? As in the Segmentations module, where one has a lot of control about opacities.

Best,
Fernando



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Opacity-of-models-slices-intersection-tp4031685.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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



_______________________________________________
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: DICOM patcher Module

Andras Lasso-2
In reply to this post by Lars Grant-West

I’ve added a new option – “Force same patient name and ID in each directory” – specifically to be able to fix the invalid DICOM files shared on morphosource.org.

 

Just download a more recent version of Slicer and follow the instructions in my earlier email:

http://slicer-users.65878.n3.nabble.com/Question-on-Image-value-range-tp4031575p4031621.html

 

Andras

 

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Lars Grant-West
Sent: February 1, 2017 9:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] DICOM patcher Module

 

I’ve been experimenting with running the DICOM Patcher module on a folder full of DICOM slices, but am finding that the module is stripping out the sequential file numbering, and puts each image into it’s own individual nest of folders, three deep.

 

As a result, image J (Fiji) won’t see the images to process them, photoshop can’t batch rename them, and I can’t seem to get them to import into 3D slicer as anything 

 

Original file directory:

cid:07421DE3-FB7D-406B-A654-600ABD615548

 

Resulting file directory after running DICOM Patcher

cid:1F66AD5C-2E7E-453C-9060-F8024E27882A

 

Result when I attempt to import resulting folder

cid:03192D1E-429D-4CC2-85B1-A1D5A66B816E

 

Is there a way to get the patcher to leave the image files in a single directory un-nested and sequentially named? 

 

 

I’ve tried unchecking the different parameters, but unless the three shown below are checked, I get an error.

 

cid:7050F38A-C527-4CDF-B8A1-7DEE55CCB35A

 

I’m still doing this in an attempt to standardize the value range in the slices so I don’t get this kind of banding.

 

cid:image009.jpg@01D27C7B.1F4409E0

 

Thanks,

 

Lars

 

 

 

 

On Jan 30, 2017, at 10:03 PM, Andras Lasso <[hidden email]> wrote:

 

Thank you for reporting this. The modification was introduced when support for volumetric mesh visualization was added recently.

For now, I've restored the original behavior (keep slice intersections 100% opaque, apply display node's opacity to 3D views only). If opaque slice intersection is not suitable for visualization of volumetric meshes then a new attribute (SliceIntersectionOpacity) should be added.

Andras

-----Original Message-----
From: slicer-users [[hidden email]] On Behalf Of Fernando Pérez-García
Sent: January 30, 2017 12:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Opacity of models/slices intersection

Hi all,

I just noticed that when one changes the opacity of a model, the opacity of its slice intersection is also modified. I think this new behavior is interesting, but not always desired. I can't find the commit that changed this.

Is there a way to link/unlink 2D and 3D opacity? As in the Segmentations module, where one has a lot of control about opacities.

Best,
Fernando



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Opacity-of-models-slices-intersection-tp4031685.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: DICOM patcher Module

Lars Grant-West
In reply to this post by Lars Grant-West
Andras - 

What service!

That solved the issue of the multiple folders caused by the bad data on Morpho handily, so thank you very much.

I still have to figure out a way to standardize the value range which is causing the banding - but it seems clear that that’s also an issue with the quality of the original data and has nothing to do with the 3D slicer software.

I believe that’s going to be a task I’ll have to find a way to automate with image editing software, or just suffer through the artifacting.

I really enjoy the detail in the data, so I think I’ll probably end up creating overlapping surface models in chunks, then importing them into Zbrush to decimate/remesh and merge the files after the individual segments are decimated.

Thanks again!

Lars


On Feb 1, 2017, at 11:14 AM, Andras Lasso <[hidden email]> wrote:

I’ve added a new option – “Force same patient name and ID in each directory” – specifically to be able to fix the invalid DICOM files shared on morphosource.org.
 
Just download a more recent version of Slicer and follow the instructions in my earlier email:
 
Andras
 
 
From: slicer-users [[hidden email]] On Behalf Of Lars Grant-West
Sent: February 1, 2017 9:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] DICOM patcher Module
 
I’ve been experimenting with running the DICOM Patcher module on a folder full of DICOM slices, but am finding that the module is stripping out the sequential file numbering, and puts each image into it’s own individual nest of folders, three deep. 
 
As a result, image J (Fiji) won’t see the images to process them, photoshop can’t batch rename them, and I can’t seem to get them to import into 3D slicer as anything 
 
Original file directory:
<image010.png>
 
Resulting file directory after running DICOM Patcher
<image011.png>
 
Result when I attempt to import resulting folder
<image012.png>
 
Is there a way to get the patcher to leave the image files in a single directory un-nested and sequentially named? 
 
 
I’ve tried unchecking the different parameters, but unless the three shown below are checked, I get an error.
 
<image013.png>
 
I’m still doing this in an attempt to standardize the value range in the slices so I don’t get this kind of banding.
 
<image009.jpg>
 
Thanks,
 
Lars
 
 
 
 
On Jan 30, 2017, at 10:03 PM, Andras Lasso <[hidden email]> wrote:
 
Thank you for reporting this. The modification was introduced when support for volumetric mesh visualization was added recently.

For now, I've restored the original behavior (keep slice intersections 100% opaque, apply display node's opacity to 3D views only). If opaque slice intersection is not suitable for visualization of volumetric meshes then a new attribute (SliceIntersectionOpacity) should be added.

Andras

-----Original Message-----
From: slicer-users [[hidden email]] On Behalf Of Fernando Pérez-García
Sent: January 30, 2017 12:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Opacity of models/slices intersection

Hi all,

I just noticed that when one changes the opacity of a model, the opacity of its slice intersection is also modified. I think this new behavior is interesting, but not always desired. I can't find the commit that changed this.

Is there a way to link/unlink 2D and 3D opacity? As in the Segmentations module, where one has a lot of control about opacities.

Best,
Fernando



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Opacity-of-models-slices-intersection-tp4031685.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: DICOM patcher Module

Andras Lasso-2
In reply to this post by Lars Grant-West

If you follow the instructions in my earlier email then you get nice and smooth surface without any postprocessing.

See the 3D-printable model that I’ve created using these steps:

https://1drv.ms/v/s!Arm_AFxB9yqHrfBrBni1eI0m13lpgg

Segmentation:

https://1drv.ms/u/s!Arm_AFxB9yqHrfB1obhrWJ5xNDIkHQ

 

Andras

 

From: Lars Grant-West [mailto:[hidden email]]
Sent: February 1, 2017 12:42
To: Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: DICOM patcher Module

 

Andras - 

 

What service!

 

That solved the issue of the multiple folders caused by the bad data on Morpho handily, so thank you very much.

 

I still have to figure out a way to standardize the value range which is causing the banding - but it seems clear that that’s also an issue with the quality of the original data and has nothing to do with the 3D slicer software.

 

I believe that’s going to be a task I’ll have to find a way to automate with image editing software, or just suffer through the artifacting.

 

I really enjoy the detail in the data, so I think I’ll probably end up creating overlapping surface models in chunks, then importing them into Zbrush to decimate/remesh and merge the files after the individual segments are decimated.

 

Thanks again!

 

Lars

 

 

On Feb 1, 2017, at 11:14 AM, Andras Lasso <[hidden email]> wrote:

 

I’ve added a new option – “Force same patient name and ID in each directory” – specifically to be able to fix the invalid DICOM files shared on morphosource.org.

 

Just download a more recent version of Slicer and follow the instructions in my earlier email:

 

Andras

 

 

From: slicer-users [[hidden email]] On Behalf Of Lars Grant-West
Sent: February 1, 2017 9:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] DICOM patcher Module

 

I’ve been experimenting with running the DICOM Patcher module on a folder full of DICOM slices, but am finding that the module is stripping out the sequential file numbering, and puts each image into it’s own individual nest of folders, three deep. 

 

As a result, image J (Fiji) won’t see the images to process them, photoshop can’t batch rename them, and I can’t seem to get them to import into 3D slicer as anything 

 

Original file directory:

<image010.png>

 

Resulting file directory after running DICOM Patcher

<image011.png>

 

Result when I attempt to import resulting folder

<image012.png>

 

Is there a way to get the patcher to leave the image files in a single directory un-nested and sequentially named? 

 

 

I’ve tried unchecking the different parameters, but unless the three shown below are checked, I get an error.

 

<image013.png>

 

I’m still doing this in an attempt to standardize the value range in the slices so I don’t get this kind of banding.

 

<image009.jpg>

 

Thanks,

 

Lars

 

 

 

 

On Jan 30, 2017, at 10:03 PM, Andras Lasso <[hidden email]> wrote:

 

Thank you for reporting this. The modification was introduced when support for volumetric mesh visualization was added recently.

For now, I've restored the original behavior (keep slice intersections 100% opaque, apply display node's opacity to 3D views only). If opaque slice intersection is not suitable for visualization of volumetric meshes then a new attribute (SliceIntersectionOpacity) should be added.

Andras

-----Original Message-----
From: slicer-users [[hidden email]] On Behalf Of Fernando Pérez-García
Sent: January 30, 2017 12:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Opacity of models/slices intersection

Hi all,

I just noticed that when one changes the opacity of a model, the opacity of its slice intersection is also modified. I think this new behavior is interesting, but not always desired. I can't find the commit that changed this.

Is there a way to link/unlink 2D and 3D opacity? As in the Segmentations module, where one has a lot of control about opacities.

Best,
Fernando



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Opacity-of-models-slices-intersection-tp4031685.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: DICOM patcher Module

Andras Lasso-2
In reply to this post by Lars Grant-West

DICOM Patcher’s “Normalize file names” option does something very similar to dicomsort, but with a fixed naming pattern (to maximize compatibility).

 

However, to fix Morphosource data sets, you need the reverse of dicomsort: changing DICOM file contents based on location in the directory tree. This operation is available in DICOM Patcher as “Force same patient name and ID in each directory” option.

 

Morphosource guys do a really nice job in scanning and sharing data, but they should fix their DICOM file exporter to make their users’ life easier. You can let them know that we would be happy to help if they were not sure what to do.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Lars Grant-West
Sent: February 1, 2017 10:02
To: Steve Pieper <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] DICOM patcher Module

 

I’ve found a lot of the files on Morphosource seem to be labeled this way.

 

Holy cow. That looks great…but after downloading, signing up for Github and looking around it looks like I’d have to code code to get this working. This is well beyond my current capabilities

 

I’ll have to look for a batch processor that will be able to do the legwork of pulling this out.

 

Thank you though. I appreciate the help.

 

Lars

 

 

On Feb 1, 2017, at 9:28 AM, Steve Pieper <[hidden email]> wrote: 

 

Hi Lars -

 

Odd that each slice appears to have a different patient ID.  Certainly that's not normal DICOM.

 

Here's a utility that might help - it allows you to create an arbitrary directory/filename convention based on any of the dicom tags:

 

https://github.com/pieper/dicomsort

 

HTH,

Steve

 

On Wed, Feb 1, 2017 at 9:10 AM, Lars Grant-West <[hidden email]> wrote:

I’ve been experimenting with running the DICOM Patcher module on a folder full of DICOM slices, but am finding that the module is stripping out the sequential file numbering, and puts each image into it’s own individual nest of folders, three deep.

 

As a result, image J (Fiji) won’t see the images to process them, photoshop can’t batch rename them, and I can’t seem to get them to import into 3D slicer as anything 

 

Original file directory:

<Screen Shot 2017-02-01 at 8.51.14 AM.png>

 

Resulting file directory after running DICOM Patcher

<Screen Shot 2017-02-01 at 8.51.07 AM.png>

 

Result when I attempt to import resulting folder

<Screen Shot 2017-02-01 at 8.55.53 AM.png>

 

Is there a way to get the patcher to leave the image files in a single directory un-nested and sequentially named? 

 

 

I’ve tried unchecking the different parameters, but unless the three shown below are checked, I get an error.

 

<Screen Shot 2017-02-01 at 9.03.00 AM.png>

 

I’m still doing this in an attempt to standardize the value range in the slices so I don’t get this kind of banding.

 

<Screen-Shot-2017-02-01-at-9.08.57-AM.jpg>

 

Thanks,

 

Lars

 

 

 

 

On Jan 30, 2017, at 10:03 PM, Andras Lasso <[hidden email]> wrote:

 

Thank you for reporting this. The modification was introduced when support for volumetric mesh visualization was added recently.

For now, I've restored the original behavior (keep slice intersections 100% opaque, apply display node's opacity to 3D views only). If opaque slice intersection is not suitable for visualization of volumetric meshes then a new attribute (SliceIntersectionOpacity) should be added.

Andras

-----Original Message-----
From: slicer-users [[hidden email]] On Behalf Of Fernando Pérez-García
Sent: January 30, 2017 12:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Opacity of models/slices intersection

Hi all,

I just noticed that when one changes the opacity of a model, the opacity of its slice intersection is also modified. I think this new behavior is interesting, but not always desired. I can't find the commit that changed this.

Is there a way to link/unlink 2D and 3D opacity? As in the Segmentations module, where one has a lot of control about opacities.

Best,
Fernando



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Opacity-of-models-slices-intersection-tp4031685.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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

 

 


_______________________________________________
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: DICOM patcher Module

Lars Grant-West
In reply to this post by Lars Grant-West
I’ll make that recommendation to them. It seems like it would make sense for them to link to your software as well.
Thank you very much for your help!

Lars


On Feb 2, 2017, at 5:09 PM, Andras Lasso <[hidden email]> wrote:

DICOM Patcher’s “Normalize file names” option does something very similar to dicomsort, but with a fixed naming pattern (to maximize compatibility).

 

However, to fix Morphosource data sets, you need the reverse of dicomsort: changing DICOM file contents based on location in the directory tree. This operation is available in DICOM Patcher as “Force same patient name and ID in each directory” option.

 

Morphosource guys do a really nice job in scanning and sharing data, but they should fix their DICOM file exporter to make their users’ life easier. You can let them know that we would be happy to help if they were not sure what to do.

 

Andras

 

From: slicer-users [[hidden email]] On Behalf Of Lars Grant-West
Sent: February 1, 2017 10:02
To: Steve Pieper <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] DICOM patcher Module

 

I’ve found a lot of the files on Morphosource seem to be labeled this way.

 

Holy cow. That looks great…but after downloading, signing up for Github and looking around it looks like I’d have to code code to get this working. This is well beyond my current capabilities

 

I’ll have to look for a batch processor that will be able to do the legwork of pulling this out.

 

Thank you though. I appreciate the help.

 

Lars

 

 

On Feb 1, 2017, at 9:28 AM, Steve Pieper <[hidden email]> wrote: 

 

Hi Lars -

 

Odd that each slice appears to have a different patient ID.  Certainly that's not normal DICOM.

 

Here's a utility that might help - it allows you to create an arbitrary directory/filename convention based on any of the dicom tags:

 

https://github.com/pieper/dicomsort

 

HTH,

Steve

 

On Wed, Feb 1, 2017 at 9:10 AM, Lars Grant-West <[hidden email]> wrote:

I’ve been experimenting with running the DICOM Patcher module on a folder full of DICOM slices, but am finding that the module is stripping out the sequential file numbering, and puts each image into it’s own individual nest of folders, three deep.

 

As a result, image J (Fiji) won’t see the images to process them, photoshop can’t batch rename them, and I can’t seem to get them to import into 3D slicer as anything 

 

Original file directory:

<Screen Shot 2017-02-01 at 8.51.14 AM.png>

 

Resulting file directory after running DICOM Patcher

<Screen Shot 2017-02-01 at 8.51.07 AM.png>

 

Result when I attempt to import resulting folder

<Screen Shot 2017-02-01 at 8.55.53 AM.png>

 

Is there a way to get the patcher to leave the image files in a single directory un-nested and sequentially named? 

 

 

I’ve tried unchecking the different parameters, but unless the three shown below are checked, I get an error.

 

<Screen Shot 2017-02-01 at 9.03.00 AM.png>

 

I’m still doing this in an attempt to standardize the value range in the slices so I don’t get this kind of banding.

 

<Screen-Shot-2017-02-01-at-9.08.57-AM.jpg>

 

Thanks,

 

Lars

 

 

 

 

On Jan 30, 2017, at 10:03 PM, Andras Lasso <[hidden email]> wrote:

 

Thank you for reporting this. The modification was introduced when support for volumetric mesh visualization was added recently.

For now, I've restored the original behavior (keep slice intersections 100% opaque, apply display node's opacity to 3D views only). If opaque slice intersection is not suitable for visualization of volumetric meshes then a new attribute (SliceIntersectionOpacity) should be added.

Andras

-----Original Message-----
From: slicer-users [[hidden email]] On Behalf Of Fernando Pérez-García
Sent: January 30, 2017 12:11
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Opacity of models/slices intersection

Hi all,

I just noticed that when one changes the opacity of a model, the opacity of its slice intersection is also modified. I think this new behavior is interesting, but not always desired. I can't find the commit that changed this.

Is there a way to link/unlink 2D and 3D opacity? As in the Segmentations module, where one has a lot of control about opacities.

Best,
Fernando



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Opacity-of-models-slices-intersection-tp4031685.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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

 

 



_______________________________________________
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