Unable to denoise tensor-q space images

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

Unable to denoise tensor-q space images

Maraka, Stefania

Hello,

 

I was reading the email that you've changed with  Hoppe, Anna L.  I am using 3D Slicer on my computer which has an operating system Windows XP 32 bit, RAM  4GB (but the computer uses only 3.21GB), Intel Core 2  CPU, E7500 Processor 2.93 GHz. I analyze Tensor-Q-Space DWI images but whenever I am trying to denoised them with Rician noise model for noise reduction, the result is black image. I assumed that this is due to my RAM memory so now I am trying to change my operating system to Windows 7 64 bit and then to upgrade my memory to 8GB. Will that work or there is something else that I have to do.

 

I really appreciate any help!

 

Thank you,

Stefania Maraka



CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.

Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy Policy and Henry Ford My Health at www.henryford.com for more detailed information. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.

_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Unable to denoise tensor-q space images

Julien Finet
hi Stephania,

Before you upgrade to a new hardware, let's first make sure the problem is not from the software itself. Btw, what Slicer version are you using ?

After executing the rician noise reduction, do you have any error in the error log dialog ?  
Then, can you try your data and process on a different machine that has a different configuration  (mac or Linux, or Windows 64bits)
Finally can you describe step by step (from Slicer startup) your actions to run the filter ?

Hth,
Julien.

On Tue, May 15, 2012 at 5:48 PM, Maraka, Stefania <[hidden email]> wrote:

Hello,

 

I was reading the email that you've changed with  Hoppe, Anna L.  I am using 3D Slicer on my computer which has an operating system Windows XP 32 bit, RAM  4GB (but the computer uses only 3.21GB), Intel Core 2  CPU, E7500 Processor 2.93 GHz. I analyze Tensor-Q-Space DWI images but whenever I am trying to denoised them with Rician noise model for noise reduction, the result is black image. I assumed that this is due to my RAM memory so now I am trying to change my operating system to Windows 7 64 bit and then to upgrade my memory to 8GB. Will that work or there is something else that I have to do.

 

I really appreciate any help!

 

Thank you,

Stefania Maraka



CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.

Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy Policy and Henry Ford My Health at www.henryford.com for more detailed information. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.

_______________________________________________
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


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Unable to denoise tensor-q space images

prao893
Hi Stefania,

At the risk of giving off a wrong impression I have of you, did you
make sure that you are viewing the newly denoised image? Sometimes
when I use the editor, or run filters; basically make changes in
general, a black screen happens to me after I have hit apply. It took
me awhile to debunk this problem, but it was a simple solution of
either hitting the "viewers field of view box" (top left) or going to
the viewer menu (clicking the little pin at the top left of the slice
views) and making sure the correct image is being viewed. Sometimes
Slicer turns the eye off (closes the eye) and you are left with a
black screen.

Again I'm sure you have accounted for this, but on the slight chance
you have not, checking this will make sure you dont pull your hair out
over this.

-Prashant



On Tue, May 15, 2012 at 5:58 PM, Julien Finet <[hidden email]> wrote:

> hi Stephania,
>
> Before you upgrade to a new hardware, let's first make sure the problem is
> not from the software itself. Btw, what Slicer version are you using ?
>
> After executing the rician noise reduction, do you have any error in the
> error log dialog ?
> Then, can you try your data and process on a different machine that has a
> different configuration  (mac or Linux, or Windows 64bits)
> Finally can you describe step by step (from Slicer startup) your actions to
> run the filter ?
>
> Hth,
> Julien.
>
> On Tue, May 15, 2012 at 5:48 PM, Maraka, Stefania <[hidden email]> wrote:
>>
>> Hello,
>>
>>
>>
>> I was reading the email that you've changed with  Hoppe, Anna L.  I am
>> using 3D Slicer on my computer which has an operating system Windows XP 32
>> bit, RAM  4GB (but the computer uses only 3.21GB), Intel Core 2  CPU, E7500
>> Processor 2.93 GHz. I analyze Tensor-Q-Space DWI images but whenever I am
>> trying to denoised them with Rician noise model for noise reduction, the
>> result is black image. I assumed that this is due to my RAM memory so now I
>> am trying to change my operating system to Windows 7 64 bit and then to
>> upgrade my memory to 8GB. Will that work or there is something else that I
>> have to do.
>>
>>
>>
>> I really appreciate any help!
>>
>>
>>
>> Thank you,
>>
>> Stefania Maraka
>>
>>
>> ________________________________
>> CONFIDENTIALITY NOTICE: This email contains information from the sender
>> that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise
>> protected from disclosure. This email is intended for use only by the person
>> or entity to whom it is addressed. If you are not the intended recipient,
>> any use, disclosure, copying, distribution, printing, or any action taken in
>> reliance on the contents of this email, is strictly prohibited. If you
>> received this email in error, please contact the sending party by reply
>> email, delete the email from your computer system and shred any paper
>> copies.
>>
>> Note to Patients: There are a number of risks you should consider before
>> using e-mail to communicate with us. See our Privacy Policy and Henry Ford
>> My Health at www.henryford.com for more detailed information. If you do not
>> believe that our policy gives you the privacy and security protection you
>> need, do not send e-mail or Internet communications to us.
>>
>> _______________________________________________
>> 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
>
>
>
> _______________________________________________
> 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
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Unable to denoise tensor-q space images

Maraka, Stefania
In reply to this post by Julien Finet

 

 

From: Maraka, Stefania
Sent: Wednesday, May 16, 2012 1:36 PM
To: 'Julien Finet'
Subject: RE: [slicer-users] Unable to denoise tensor-q space images

 

Hello Julien,

 

The version of Slicer I am using is Slicer3 3.6.2010-11-03. Please see below the steps that I follow for filtering the images.

 

 

1.       Convert DWI Dicom images to NRRD format using Dicom to Nrrd Convertor module

a.       Set Input Dicom Data which is where the images are located at

b.      Set Output Directory

c.       Set Output Filename (use *_DWI in the name)

d.      Click Apply

e.      It generates and saves the volume

2.       Load the DWI Nrrd file using Volumes module

a.       Use Select Volume File to select the file created in step 1

b.      Image Origin to From File

c.       Click Apply

d.      Go to Diffusion Editor Window that has been created and check the Gradient values. Usually they are correct

3.       Filter the DWI for noise reduction using Joint Rician LMMSE Image Filter module

a.       Set Input Volume

b.      Set Output Volume (create a new one and rename is as *_DWI_Denoised)

c.       Click Apply

d.      Save the denoised volume

e.      Go to Data module and delete the DWI node, since we will work with the denoised one

There is no error message! It mentions status completed. I don't know if it is helpful but it also mentions Bg: out of frame. I have tried in my laptop before that has Windows 7 64 bit RAM 4GB but I had the same result. It was only a computer that I was able to complete the filtering successfully who had RAM memory 8 GB but I do not know what was the operating system.

 

Thanks,

Stefania

 

 

 

 

From: Julien Finet [mailto:[hidden email]]
Sent: Tuesday, May 15, 2012 5:58 PM
To: Maraka, Stefania
Cc: [hidden email]
Subject: Re: [slicer-users] Unable to denoise tensor-q space images

 

hi Stephania,

 

Before you upgrade to a new hardware, let's first make sure the problem is not from the software itself. Btw, what Slicer version are you using ?

 

After executing the rician noise reduction, do you have any error in the error log dialog ?  

Then, can you try your data and process on a different machine that has a different configuration  (mac or Linux, or Windows 64bits)

Finally can you describe step by step (from Slicer startup) your actions to run the filter ?

 

Hth,

Julien.

On Tue, May 15, 2012 at 5:48 PM, Maraka, Stefania <[hidden email]> wrote:

Hello,

 

I was reading the email that you've changed with  Hoppe, Anna L.  I am using 3D Slicer on my computer which has an operating system Windows XP 32 bit, RAM  4GB (but the computer uses only 3.21GB), Intel Core 2  CPU, E7500 Processor 2.93 GHz. I analyze Tensor-Q-Space DWI images but whenever I am trying to denoised them with Rician noise model for noise reduction, the result is black image. I assumed that this is due to my RAM memory so now I am trying to change my operating system to Windows 7 64 bit and then to upgrade my memory to 8GB. Will that work or there is something else that I have to do.

 

I really appreciate any help!

 

Thank you,

Stefania Maraka

 


CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.

Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy Policy and Henry Ford My Health at www.henryford.com for more detailed information. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.


_______________________________________________
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

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Unable to denies tensor-q space images

Maraka, Stefania
In reply to this post by prao893


-----Original Message-----
From: Maraka, Stefania
Sent: Wednesday, May 16, 2012 2:03 PM
To: 'Prashant Rao'
Cc: 'Julien Finet'
Subject: RE: [slicer-users] Unable to denies tensor-q space images

Hello, Prashant,

I have checked that. In the background layer the new denoised image is being selected. I am able to see as well the number of the slices and the distance of the slice from the RAS origin but the image is black. I have also saved the image, closed 3D Slicer and uploaded again the denoised image but I had the same result..again black image with all the other information of the image available!

Thank you!!

Stef

-----Original Message-----
From: Prashant Rao [mailto:[hidden email]]
Sent: Tuesday, May 15, 2012 7:01 PM
To: Julien Finet
Cc: Maraka, Stefania; [hidden email]
Subject: Re: [slicer-users] Unable to denoise tensor-q space images

Hi Stefania,

At the risk of giving off a wrong impression I have of you, did you
make sure that you are viewing the newly denoised image? Sometimes
when I use the editor, or run filters; basically make changes in
general, a black screen happens to me after I have hit apply. It took
me awhile to debunk this problem, but it was a simple solution of
either hitting the "viewers field of view box" (top left) or going to
the viewer menu (clicking the little pin at the top left of the slice
views) and making sure the correct image is being viewed. Sometimes
Slicer turns the eye off (closes the eye) and you are left with a
black screen.

Again I'm sure you have accounted for this, but on the slight chance
you have not, checking this will make sure you dont pull your hair out
over this.

-Prashant



On Tue, May 15, 2012 at 5:58 PM, Julien Finet <[hidden email]> wrote:

> hi Stephania,
>
> Before you upgrade to a new hardware, let's first make sure the problem is
> not from the software itself. Btw, what Slicer version are you using ?
>
> After executing the rician noise reduction, do you have any error in the
> error log dialog ?
> Then, can you try your data and process on a different machine that has a
> different configuration  (mac or Linux, or Windows 64bits)
> Finally can you describe step by step (from Slicer startup) your actions to
> run the filter ?
>
> Hth,
> Julien.
>
> On Tue, May 15, 2012 at 5:48 PM, Maraka, Stefania <[hidden email]> wrote:
>>
>> Hello,
>>
>>
>>
>> I was reading the email that you've changed with  Hoppe, Anna L.  I am
>> using 3D Slicer on my computer which has an operating system Windows XP 32
>> bit, RAM  4GB (but the computer uses only 3.21GB), Intel Core 2  CPU, E7500
>> Processor 2.93 GHz. I analyze Tensor-Q-Space DWI images but whenever I am
>> trying to denoised them with Rician noise model for noise reduction, the
>> result is black image. I assumed that this is due to my RAM memory so now I
>> am trying to change my operating system to Windows 7 64 bit and then to
>> upgrade my memory to 8GB. Will that work or there is something else that I
>> have to do.
>>
>>
>>
>> I really appreciate any help!
>>
>>
>>
>> Thank you,
>>
>> Stefania Maraka
>>
>>
>> ________________________________
>> CONFIDENTIALITY NOTICE: This email contains information from the sender
>> that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise
>> protected from disclosure. This email is intended for use only by the person
>> or entity to whom it is addressed. If you are not the intended recipient,
>> any use, disclosure, copying, distribution, printing, or any action taken in
>> reliance on the contents of this email, is strictly prohibited. If you
>> received this email in error, please contact the sending party by reply
>> email, delete the email from your computer system and shred any paper
>> copies.
>>
>> Note to Patients: There are a number of risks you should consider before
>> using e-mail to communicate with us. See our Privacy Policy and Henry Ford
>> My Health at www.henryford.com for more detailed information. If you do not
>> believe that our policy gives you the privacy and security protection you
>> need, do not send e-mail or Internet communications to us.
>>
>> _______________________________________________
>> 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
>
>
>
> _______________________________________________
> 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
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Unable to denoise tensor-q space images

Maraka, Stefania
In reply to this post by Maraka, Stefania

Hello,

 

I have checked the two computers that the step of denoining  is completed right. It is one computer that has Windows Vista Ultimate 64 bit with 8GB RAM, nVida Quadro NVS 290 graphic card and one other that has  Windows XP 32 bit, 4GB RAM, nVidia Quadro NVS 285 graphic card. My computer has Windows XP 32 bit, 4GB RAM, Intel 4 series Express Chipes Family graphic card and when I denoised the DWI (Tensor Q Space, 56 directions , 241 MB, 1.769 files) the result is black image. It seems that it is completed and I can see all the information of the DWi like how many slices I have, the Bg components e.t.c but the image is black. Instead, When I am working with the first two computer that I have mentioned with the same data, the denoising step works right.

 

I have already bought an extra RAM memory to upgrade from 4GB to 8GB but first I have to change my operating system from 32 bit to 64 bit. Should I do that or I should change my graphic card.

 

I really appreciate any help on this!

 

Thanks,

Stefania

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Maraka, Stefania
Sent: Wednesday, May 16, 2012 2:07 PM
To: 'Julien Finet'
Cc: [hidden email]
Subject: Re: [slicer-users] Unable to denoise tensor-q space images

 

 

 

From: Maraka, Stefania
Sent: Wednesday, May 16, 2012 1:36 PM
To: 'Julien Finet'
Subject: RE: [slicer-users] Unable to denoise tensor-q space images

 

Hello Julien,

 

The version of Slicer I am using is Slicer3 3.6.2010-11-03. Please see below the steps that I follow for filtering the images.

 

 

1.       Convert DWI Dicom images to NRRD format using Dicom to Nrrd Convertor module

a.       Set Input Dicom Data which is where the images are located at

b.      Set Output Directory

c.       Set Output Filename (use *_DWI in the name)

d.      Click Apply

e.      It generates and saves the volume

2.       Load the DWI Nrrd file using Volumes module

a.       Use Select Volume File to select the file created in step 1

b.      Image Origin to From File

c.       Click Apply

d.      Go to Diffusion Editor Window that has been created and check the Gradient values. Usually they are correct

3.       Filter the DWI for noise reduction using Joint Rician LMMSE Image Filter module

a.       Set Input Volume

b.      Set Output Volume (create a new one and rename is as *_DWI_Denoised)

c.       Click Apply

d.      Save the denoised volume

e.      Go to Data module and delete the DWI node, since we will work with the denoised one

There is no error message! It mentions status completed. I don't know if it is helpful but it also mentions Bg: out of frame. I have tried in my laptop before that has Windows 7 64 bit RAM 4GB but I had the same result. It was only a computer that I was able to complete the filtering successfully who had RAM memory 8 GB but I do not know what was the operating system.

 

Thanks,

Stefania

 

 

 

 

From: Julien Finet [mailto:[hidden email]]
Sent: Tuesday, May 15, 2012 5:58 PM
To: Maraka, Stefania
Cc: [hidden email]
Subject: Re: [slicer-users] Unable to denoise tensor-q space images

 

hi Stephania,

 

Before you upgrade to a new hardware, let's first make sure the problem is not from the software itself. Btw, what Slicer version are you using ?

 

After executing the rician noise reduction, do you have any error in the error log dialog ?  

Then, can you try your data and process on a different machine that has a different configuration  (mac or Linux, or Windows 64bits)

Finally can you describe step by step (from Slicer startup) your actions to run the filter ?

 

Hth,

Julien.

On Tue, May 15, 2012 at 5:48 PM, Maraka, Stefania <[hidden email]> wrote:

Hello,

 

I was reading the email that you've changed with  Hoppe, Anna L.  I am using 3D Slicer on my computer which has an operating system Windows XP 32 bit, RAM  4GB (but the computer uses only 3.21GB), Intel Core 2  CPU, E7500 Processor 2.93 GHz. I analyze Tensor-Q-Space DWI images but whenever I am trying to denoised them with Rician noise model for noise reduction, the result is black image. I assumed that this is due to my RAM memory so now I am trying to change my operating system to Windows 7 64 bit and then to upgrade my memory to 8GB. Will that work or there is something else that I have to do.

 

I really appreciate any help!

 

Thank you,

Stefania Maraka

 


CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.

Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy Policy and Henry Ford My Health at www.henryford.com for more detailed information. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.


_______________________________________________
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

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Unable to denoise tensor-q space images

Steve Pieper
Hi Stefania -

Your graphics card shouldn't have any influence on the denoising filter.  But memory allocation in the operating system certainly can.  Did you check the error log for messages from the filter?  As a general rule we suggest using a 64 bit OS and 64 bit version of slicer.

Best,
Steve

On Wed, May 23, 2012 at 10:45 AM, Maraka, Stefania <[hidden email]> wrote:

Hello,

 

I have checked the two computers that the step of denoining  is completed right. It is one computer that has Windows Vista Ultimate 64 bit with 8GB RAM, nVida Quadro NVS 290 graphic card and one other that has  Windows XP 32 bit, 4GB RAM, nVidia Quadro NVS 285 graphic card. My computer has Windows XP 32 bit, 4GB RAM, Intel 4 series Express Chipes Family graphic card and when I denoised the DWI (Tensor Q Space, 56 directions , 241 MB, 1.769 files) the result is black image. It seems that it is completed and I can see all the information of the DWi like how many slices I have, the Bg components e.t.c but the image is black. Instead, When I am working with the first two computer that I have mentioned with the same data, the denoising step works right.

 

I have already bought an extra RAM memory to upgrade from 4GB to 8GB but first I have to change my operating system from 32 bit to 64 bit. Should I do that or I should change my graphic card.

 

I really appreciate any help on this!

 

Thanks,

Stefania

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Maraka, Stefania
Sent: Wednesday, May 16, 2012 2:07 PM
To: 'Julien Finet'


Cc: [hidden email]
Subject: Re: [slicer-users] Unable to denoise tensor-q space images

 

 

 

From: Maraka, Stefania
Sent: Wednesday, May 16, 2012 1:36 PM
To: 'Julien Finet'
Subject: RE: [slicer-users] Unable to denoise tensor-q space images

 

Hello Julien,

 

The version of Slicer I am using is Slicer3 3.6.2010-11-03. Please see below the steps that I follow for filtering the images.

 

 

1.       Convert DWI Dicom images to NRRD format using Dicom to Nrrd Convertor module

a.       Set Input Dicom Data which is where the images are located at

b.      Set Output Directory

c.       Set Output Filename (use *_DWI in the name)

d.      Click Apply

e.      It generates and saves the volume

2.       Load the DWI Nrrd file using Volumes module

a.       Use Select Volume File to select the file created in step 1

b.      Image Origin to From File

c.       Click Apply

d.      Go to Diffusion Editor Window that has been created and check the Gradient values. Usually they are correct

3.       Filter the DWI for noise reduction using Joint Rician LMMSE Image Filter module

a.       Set Input Volume

b.      Set Output Volume (create a new one and rename is as *_DWI_Denoised)

c.       Click Apply

d.      Save the denoised volume

e.      Go to Data module and delete the DWI node, since we will work with the denoised one

There is no error message! It mentions status completed. I don't know if it is helpful but it also mentions Bg: out of frame. I have tried in my laptop before that has Windows 7 64 bit RAM 4GB but I had the same result. It was only a computer that I was able to complete the filtering successfully who had RAM memory 8 GB but I do not know what was the operating system.

 

Thanks,

Stefania

 

 

 

 

From: Julien Finet [mailto:[hidden email]]
Sent: Tuesday, May 15, 2012 5:58 PM
To: Maraka, Stefania
Cc: [hidden email]
Subject: Re: [slicer-users] Unable to denoise tensor-q space images

 

hi Stephania,

 

Before you upgrade to a new hardware, let's first make sure the problem is not from the software itself. Btw, what Slicer version are you using ?

 

After executing the rician noise reduction, do you have any error in the error log dialog ?  

Then, can you try your data and process on a different machine that has a different configuration  (mac or Linux, or Windows 64bits)

Finally can you describe step by step (from Slicer startup) your actions to run the filter ?

 

Hth,

Julien.

On Tue, May 15, 2012 at 5:48 PM, Maraka, Stefania <[hidden email]> wrote:

Hello,

 

I was reading the email that you've changed with  Hoppe, Anna L.  I am using 3D Slicer on my computer which has an operating system Windows XP 32 bit, RAM  4GB (but the computer uses only 3.21GB), Intel Core 2  CPU, E7500 Processor 2.93 GHz. I analyze Tensor-Q-Space DWI images but whenever I am trying to denoised them with Rician noise model for noise reduction, the result is black image. I assumed that this is due to my RAM memory so now I am trying to change my operating system to Windows 7 64 bit and then to upgrade my memory to 8GB. Will that work or there is something else that I have to do.

 

I really appreciate any help!

 

Thank you,

Stefania Maraka

 


CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.

Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy Policy and Henry Ford My Health at www.henryford.com for more detailed information. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.


_______________________________________________
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

 


_______________________________________________
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


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Unable to denoise tensor-q space images

Maraka, Stefania

Hello Steve,

 

Thank you so much for the help. I didn't get any error message. Is it smth that I need to search? But in that case what makes the difference between my vcomputer and the computer that has Windows XP 32 bit, 4GB RAM, nVidia Quadro NVS 285 graphic card? I mean I should have faced the same problen on that computer as well right?

 

Thanks,

Stef

 

From: Steve Pieper [mailto:[hidden email]]
Sent: Wednesday, May 23, 2012 2:32 PM
To: Maraka, Stefania
Cc: Julien Finet; Prashant Rao; [hidden email]
Subject: Re: [slicer-users] Unable to denoise tensor-q space images

 

Hi Stefania -

Your graphics card shouldn't have any influence on the denoising filter.  But memory allocation in the operating system certainly can.  Did you check the error log for messages from the filter?  As a general rule we suggest using a 64 bit OS and 64 bit version of slicer.

Best,
Steve

On Wed, May 23, 2012 at 10:45 AM, Maraka, Stefania <[hidden email]> wrote:

Hello,

 

I have checked the two computers that the step of denoining  is completed right. It is one computer that has Windows Vista Ultimate 64 bit with 8GB RAM, nVida Quadro NVS 290 graphic card and one other that has  Windows XP 32 bit, 4GB RAM, nVidia Quadro NVS 285 graphic card. My computer has Windows XP 32 bit, 4GB RAM, Intel 4 series Express Chipes Family graphic card and when I denoised the DWI (Tensor Q Space, 56 directions , 241 MB, 1.769 files) the result is black image. It seems that it is completed and I can see all the information of the DWi like how many slices I have, the Bg components e.t.c but the image is black. Instead, When I am working with the first two computer that I have mentioned with the same data, the denoising step works right.

 

I have already bought an extra RAM memory to upgrade from 4GB to 8GB but first I have to change my operating system from 32 bit to 64 bit. Should I do that or I should change my graphic card.

 

I really appreciate any help on this!

 

Thanks,

Stefania

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Maraka, Stefania
Sent: Wednesday, May 16, 2012 2:07 PM
To: 'Julien Finet'


Cc: [hidden email]
Subject: Re: [slicer-users] Unable to denoise tensor-q space images

 

 

 

From: Maraka, Stefania
Sent: Wednesday, May 16, 2012 1:36 PM
To: 'Julien Finet'
Subject: RE: [slicer-users] Unable to denoise tensor-q space images

 

Hello Julien,

 

The version of Slicer I am using is Slicer3 3.6.2010-11-03. Please see below the steps that I follow for filtering the images.

 

 

1.       Convert DWI Dicom images to NRRD format using Dicom to Nrrd Convertor module

a.       Set Input Dicom Data which is where the images are located at

b.      Set Output Directory

c.       Set Output Filename (use *_DWI in the name)

d.      Click Apply

e.      It generates and saves the volume

2.       Load the DWI Nrrd file using Volumes module

a.       Use Select Volume File to select the file created in step 1

b.      Image Origin to From File

c.       Click Apply

d.      Go to Diffusion Editor Window that has been created and check the Gradient values. Usually they are correct

3.       Filter the DWI for noise reduction using Joint Rician LMMSE Image Filter module

a.       Set Input Volume

b.      Set Output Volume (create a new one and rename is as *_DWI_Denoised)

c.       Click Apply

d.      Save the denoised volume

e.      Go to Data module and delete the DWI node, since we will work with the denoised one

There is no error message! It mentions status completed. I don't know if it is helpful but it also mentions Bg: out of frame. I have tried in my laptop before that has Windows 7 64 bit RAM 4GB but I had the same result. It was only a computer that I was able to complete the filtering successfully who had RAM memory 8 GB but I do not know what was the operating system.

 

Thanks,

Stefania

 

 

 

 

From: Julien Finet [mailto:[hidden email]]
Sent: Tuesday, May 15, 2012 5:58 PM
To: Maraka, Stefania
Cc: [hidden email]
Subject: Re: [slicer-users] Unable to denoise tensor-q space images

 

hi Stephania,

 

Before you upgrade to a new hardware, let's first make sure the problem is not from the software itself. Btw, what Slicer version are you using ?

 

After executing the rician noise reduction, do you have any error in the error log dialog ?  

Then, can you try your data and process on a different machine that has a different configuration  (mac or Linux, or Windows 64bits)

Finally can you describe step by step (from Slicer startup) your actions to run the filter ?

 

Hth,

Julien.

On Tue, May 15, 2012 at 5:48 PM, Maraka, Stefania <[hidden email]> wrote:

Hello,

 

I was reading the email that you've changed with  Hoppe, Anna L.  I am using 3D Slicer on my computer which has an operating system Windows XP 32 bit, RAM  4GB (but the computer uses only 3.21GB), Intel Core 2  CPU, E7500 Processor 2.93 GHz. I analyze Tensor-Q-Space DWI images but whenever I am trying to denoised them with Rician noise model for noise reduction, the result is black image. I assumed that this is due to my RAM memory so now I am trying to change my operating system to Windows 7 64 bit and then to upgrade my memory to 8GB. Will that work or there is something else that I have to do.

 

I really appreciate any help!

 

Thank you,

Stefania Maraka

 


CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.

Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy Policy and Henry Ford My Health at www.henryford.com for more detailed information. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.


_______________________________________________
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

 


_______________________________________________
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

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Unable to denoise tensor-q space images

Steve Pieper
Hi Stef -

It's really hard to say for sure, but sometimes windows will have strange memory allocation behavior - for example a device driver or other program might be taking up space in the middle of memory such that no other program can allocate a contiguous block. 

-Steve

On Wed, May 23, 2012 at 2:45 PM, Maraka, Stefania <[hidden email]> wrote:

Hello Steve,

 

Thank you so much for the help. I didn't get any error message. Is it smth that I need to search? But in that case what makes the difference between my vcomputer and the computer that has Windows XP 32 bit, 4GB RAM, nVidia Quadro NVS 285 graphic card? I mean I should have faced the same problen on that computer as well right?

 

Thanks,

Stef

 

From: Steve Pieper [mailto:[hidden email]]
Sent: Wednesday, May 23, 2012 2:32 PM
To: Maraka, Stefania
Cc: Julien Finet; Prashant Rao; [hidden email]


Subject: Re: [slicer-users] Unable to denoise tensor-q space images

 

Hi Stefania -

Your graphics card shouldn't have any influence on the denoising filter.  But memory allocation in the operating system certainly can.  Did you check the error log for messages from the filter?  As a general rule we suggest using a 64 bit OS and 64 bit version of slicer.

Best,
Steve

On Wed, May 23, 2012 at 10:45 AM, Maraka, Stefania <[hidden email]> wrote:

Hello,

 

I have checked the two computers that the step of denoining  is completed right. It is one computer that has Windows Vista Ultimate 64 bit with 8GB RAM, nVida Quadro NVS 290 graphic card and one other that has  Windows XP 32 bit, 4GB RAM, nVidia Quadro NVS 285 graphic card. My computer has Windows XP 32 bit, 4GB RAM, Intel 4 series Express Chipes Family graphic card and when I denoised the DWI (Tensor Q Space, 56 directions , 241 MB, 1.769 files) the result is black image. It seems that it is completed and I can see all the information of the DWi like how many slices I have, the Bg components e.t.c but the image is black. Instead, When I am working with the first two computer that I have mentioned with the same data, the denoising step works right.

 

I have already bought an extra RAM memory to upgrade from 4GB to 8GB but first I have to change my operating system from 32 bit to 64 bit. Should I do that or I should change my graphic card.

 

I really appreciate any help on this!

 

Thanks,

Stefania

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Maraka, Stefania
Sent: Wednesday, May 16, 2012 2:07 PM
To: 'Julien Finet'


Cc: [hidden email]
Subject: Re: [slicer-users] Unable to denoise tensor-q space images

 

 

 

From: Maraka, Stefania
Sent: Wednesday, May 16, 2012 1:36 PM
To: 'Julien Finet'
Subject: RE: [slicer-users] Unable to denoise tensor-q space images

 

Hello Julien,

 

The version of Slicer I am using is Slicer3 3.6.2010-11-03. Please see below the steps that I follow for filtering the images.

 

 

1.       Convert DWI Dicom images to NRRD format using Dicom to Nrrd Convertor module

a.       Set Input Dicom Data which is where the images are located at

b.      Set Output Directory

c.       Set Output Filename (use *_DWI in the name)

d.      Click Apply

e.      It generates and saves the volume

2.       Load the DWI Nrrd file using Volumes module

a.       Use Select Volume File to select the file created in step 1

b.      Image Origin to From File

c.       Click Apply

d.      Go to Diffusion Editor Window that has been created and check the Gradient values. Usually they are correct

3.       Filter the DWI for noise reduction using Joint Rician LMMSE Image Filter module

a.       Set Input Volume

b.      Set Output Volume (create a new one and rename is as *_DWI_Denoised)

c.       Click Apply

d.      Save the denoised volume

e.      Go to Data module and delete the DWI node, since we will work with the denoised one

There is no error message! It mentions status completed. I don't know if it is helpful but it also mentions Bg: out of frame. I have tried in my laptop before that has Windows 7 64 bit RAM 4GB but I had the same result. It was only a computer that I was able to complete the filtering successfully who had RAM memory 8 GB but I do not know what was the operating system.

 

Thanks,

Stefania

 

 

 

 

From: Julien Finet [mailto:[hidden email]]
Sent: Tuesday, May 15, 2012 5:58 PM
To: Maraka, Stefania
Cc: [hidden email]
Subject: Re: [slicer-users] Unable to denoise tensor-q space images

 

hi Stephania,

 

Before you upgrade to a new hardware, let's first make sure the problem is not from the software itself. Btw, what Slicer version are you using ?

 

After executing the rician noise reduction, do you have any error in the error log dialog ?  

Then, can you try your data and process on a different machine that has a different configuration  (mac or Linux, or Windows 64bits)

Finally can you describe step by step (from Slicer startup) your actions to run the filter ?

 

Hth,

Julien.

On Tue, May 15, 2012 at 5:48 PM, Maraka, Stefania <[hidden email]> wrote:

Hello,

 

I was reading the email that you've changed with  Hoppe, Anna L.  I am using 3D Slicer on my computer which has an operating system Windows XP 32 bit, RAM  4GB (but the computer uses only 3.21GB), Intel Core 2  CPU, E7500 Processor 2.93 GHz. I analyze Tensor-Q-Space DWI images but whenever I am trying to denoised them with Rician noise model for noise reduction, the result is black image. I assumed that this is due to my RAM memory so now I am trying to change my operating system to Windows 7 64 bit and then to upgrade my memory to 8GB. Will that work or there is something else that I have to do.

 

I really appreciate any help!

 

Thank you,

Stefania Maraka

 


CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.

Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy Policy and Henry Ford My Health at www.henryford.com for more detailed information. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.


_______________________________________________
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

 


_______________________________________________
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

 



_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Unable to denoise tensor-q space images

Demian Wassermann-2
In reply to this post by Maraka, Stefania
Hello Stefania,

This is a bug in the latest version of Slicer, we are working to correct it. You can follow the status of this bug here:


Sorry about the inconvenience!

Best
Demian
--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On May 15, 2012, at 5:48 PM, Maraka, Stefania wrote:

Hello,
 
I was reading the email that you've changed with  Hoppe, Anna L.  I am using 3D Slicer on my computer which has an operating system Windows XP 32 bit, RAM  4GB (but the computer uses only 3.21GB), Intel Core 2  CPU, E7500 Processor 2.93 GHz. I analyze Tensor-Q-Space DWI images but whenever I am trying to denoised them with Rician noise model for noise reduction, the result is black image. I assumed that this is due to my RAM memory so now I am trying to change my operating system to Windows 7 64 bit and then to upgrade my memory to 8GB. Will that work or there is something else that I have to do.
 
I really appreciate any help!
 
Thank you,
Stefania Maraka


CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.

Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy Policy and Henry Ford My Health at www.henryford.com for more detailed information. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.
_______________________________________________
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


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Unable to denoise tensor-q space images

Demian Wassermann-2
Hello Stefania. The issue should be fixed.

You should be able to get it from the last nightly build

D

--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On May 23, 2012, at 6:30 PM, Demian Wassermann wrote:

Hello Stefania,

This is a bug in the latest version of Slicer, we are working to correct it. You can follow the status of this bug here:


Sorry about the inconvenience!

Best
Demian
--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On May 15, 2012, at 5:48 PM, Maraka, Stefania wrote:

Hello,
 
I was reading the email that you've changed with  Hoppe, Anna L.  I am using 3D Slicer on my computer which has an operating system Windows XP 32 bit, RAM  4GB (but the computer uses only 3.21GB), Intel Core 2  CPU, E7500 Processor 2.93 GHz. I analyze Tensor-Q-Space DWI images but whenever I am trying to denoised them with Rician noise model for noise reduction, the result is black image. I assumed that this is due to my RAM memory so now I am trying to change my operating system to Windows 7 64 bit and then to upgrade my memory to 8GB. Will that work or there is something else that I have to do.
 
I really appreciate any help!
 
Thank you,
Stefania Maraka


CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.

Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy Policy and Henry Ford My Health at www.henryford.com for more detailed information. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.
_______________________________________________
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

_______________________________________________
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


_______________________________________________
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