[slicer-users] slicer-users Digest, Vol 76, Issue 16

David Kamson promeoso at hotmail.com
Mon Aug 1 14:49:07 EDT 2011


Question on brain mask extraction

Hello Slicer Community!

I have problems with extracting brain masks from MRI images.
I am using the current stable version, and I could not make
neither Extract Skeleton, nor Skull Stripper work.
I'd mainly use MPRAGE, and regular T1-weighted images.
Is it a widespread issue?

Thanks in advance,
David Kamson, MD

> From: slicer-users-request at bwh.harvard.edu
> Subject: slicer-users Digest, Vol 76, Issue 16
> To: slicer-users at bwh.harvard.edu
> Date: Fri, 29 Jul 2011 09:09:57 -0400
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> Today's Topics:
> 
>    1. Fwd:  firts steps in tractography (Tatjana Polgar)
>    2. Re: firts steps in tractography (cvalencia)
>    3.  Fwd: firts steps in tractography (Thomas Ballinger)
>    4. Fw: Fw:  Fwd: firts steps in tractography (Tatjana Polgar)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 28 Jul 2011 09:24:25 -0700 (PDT)
> From: Tatjana Polgar <tanyapolgar at yahoo.com>
> Subject: [slicer-users] Fwd:  firts steps in tractography
> To: slicer-user <slicer-users at bwh.harvard.edu>
> Message-ID:
> 	<1311870265.16615.YahooMailNeo at web38206.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hello Slicer Users!
> I have similar problems with our 3 T HDx GE scanner as Carolina.
> Even on my non-anomyzed DWI images gradient values come through as: 0-0-0.
> Is there a way to get the gradients as a text file as I noticed txt file could be loaded into slicer?
> Thank you!
> Tatjana
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> ------------------------------
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> Message: 2
> Date: Thu, 28 Jul 2011 09:42:32 -0700 (PDT)
> From: cvalencia <cvalencia at linkdx.com.co>
> Subject: Re: [slicer-users] firts steps in tractography
> To: slicer-users at bwh.harvard.edu
> Message-ID:
> 	<CANoyBY846ufF930QAtokkY9SM4bPxnsSgURMWTLuXryDHKUQ_g at mail.gmail.com>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi Xiaodong,
> 
> Thanks for your reply.
> I use the diffusion tensor estimation module I can run it but show a message
> finish with errors, and I can not see the outputs in the 2d views, i.e the
> blue mask.
> 
> Thanks,
> 
> Carolina
> 
> 2011/7/28 Xiaodong Tao-3 [via slicer-users] <
> ml-node+3206982-977666563-236622 at n3.nabble.com>
> 
> > Hello Carolina,
> >
> > That is because the images were acquired in oblique planes. The default
> > view mode in Slicer is axial/coronal/sagittal. Please see if you are able to
> > do tractography using the converted nrrd file.
> >
> > Hope this helps,
> > Xiaodong
> >
> > On Jul 28, 2011, at 11:17 AM, Carolina Valencia wrote:
> >
> > Hi Steve,
> >
> > Thanks for your reply.
> > I used the tool you mention but when I see it in the volumes module and
> > play with the window level, I noticed in the beginning an in the end of the
> > slices in the tree views a few slices cut in diagonal.
> > Then, when I use the diffusion tensor estimation module I can run it but
> > show a message finish with errors, and I can not see the outputs in the 2d
> > views, i.e the blue mask.
> >
> > Thanks,
> >
> > Carolina
> >
> > 2011/7/28 Steve Pieper <[hidden email]<http://user/SendEmail.jtp?type=node&node=3206982&i=0>
> > >
> >
> >> Hi Carolina -
> >>
> >> Did you run the DicomToNrrd tool?  This is what we usually use to convert
> >> the scanner data into a format compatible with slicer:
> >>
> >> http://www.slicer.org/slicerWiki/index.php/Modules:DicomToNRRD-3.6
> >>
> >> Then you should be able to follow the steps in the Diffution MRI tutorial.
> >>
> >> HTH,
> >> Steve
> >>
> >> On Thu, Jul 28, 2011 at 10:43 AM, Carolina Valencia <[hidden email]<http://user/SendEmail.jtp?type=node&node=3206982&i=1>
> >> > wrote:
> >>
> >>> Hello Slicer users,
> >>>
> >>> I would like to perform tractography on my own data, but I'm uck in the
> >>> very first step. I add the DICOM serie from the scanner (GE Signa 1.5T) the
> >>> protocol's names are TENSOR ASSET and DIFFUSION DWI, I assume is the last
> >>> one, when I load it, the axial view is correct, but the other two views
> >>> shown 2 images, one below to the other, it seems the b0 is extracted from
> >>> the other ones. Then I converted them in dcm2nii, and I load the .nii.gz
> >>> file, and the views are correct, but when I start with the diffusion tensor
> >>> estimation, I can not choose any option in Input DWI volume, my voume loaded
> >>> doesn't appear in the list.
> >>>
> >>> Thanks for your help,
> >>>
> >>> Best regards,
> >>>
> >>> Carolina
> >>>
> >>> _______________________________________________
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> >>>
> >>
> >>
> >
> >
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> ------------------------------
> 
> Message: 3
> Date: Thu, 28 Jul 2011 15:44:49 -0400
> From: Thomas Ballinger <tomb at bwh.harvard.edu>
> Subject: [slicer-users]  Fwd: firts steps in tractography
> To: slicer-users at bwh.harvard.edu
> Message-ID:
> 	<CABb6=DUpFP5j=i82hCuA29HAW6VVOWr-9i9LDxKPW791MTwb+Q at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Yes, I have used the module: Convert Dicom to Nrrd.
> I have attached the text message that slicer provided me with after the
> convert.
> Is there anything else that I can try to obtain the gradient info ?
> 
> Thanks
> Tatjana
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> ImageOrientationPatient (0020|0032): 0.996649\-0.0218514\0.0788297\-0.0137028\0.905419\0.424297\
> ==================================
> Direction Cosines: 
> 0.996649 -0.0137028 -0.0806454
> -0.0218514 0.905419 -0.423955
> 0.0788297 0.424297 0.902086
> 
> ==================================
> MeasurementFrame: 
> 0.996649 -0.0137028 -0.0806454
> -0.0218514 0.905419 -0.423955
> 0.0788297 0.424297 0.902086
> 
> ==================================
> DWMRI_gradient_0000=[-0;-0;0]
> DWMRI_gradient_0001=[0;0;0]
> ==================================
> Protocol_gradient_0000=[0;0;0]
> Protocol_gradient_0001=[0;0;0]
> ==================================
> 
> ------------------------------
> 
> Message: 4
> Date: Fri, 29 Jul 2011 10:13:53 -0700 (PDT)
> From: Tatjana Polgar <tanyapolgar at yahoo.com>
> Subject: [slicer-users] Fw: Fw:  Fwd: firts steps in tractography
> To: slicer-user <slicer-users at bwh.harvard.edu>
> Message-ID:
> 	<1311959633.68395.YahooMailNeo at web38205.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Thank you Thomas!
> Yes, I have used the module: Conver Dicom to Nrrd. 
> I have attached the text message that slicer provided me with after the convert. 
> Is there anything else that I can try to obtain the gradient info ?
> 
> 
> Thanks
> Tatjana
> 
> 
> 
> 
> 
> 
> 
> ----- Forwarded Message -----
> >
> >From: Thomas Ballinger <tomb at bwh.harvard.edu>
> >To: Tatjana Polgar <tanyapolgar at yahoo.com>
> >Sent: Thursday, July 28, 2011 11:29 AM
> >Subject: Re: [slicer-users] Fwd: firts steps in tractography
> >
> >
> >Have you used the Dicom2Nrrd module yet?? Give that a try, it's much better at creating diffusion nrrds than loading the volume via "Load Volume".
> >
> >
> >On Thu, Jul 28, 2011 at 12:24 PM, Tatjana Polgar <tanyapolgar at yahoo.com> wrote:
> >
> >Hello Slicer Users!
> >>I have similar problems with our 3 T HDx GE scanner as Carolina.
> >>Even on my non-anomyzed DWI images gradient values come through as: 0-0-0.
> >>Is there a way to get the gradients as a text file as I noticed txt file could be loaded into slicer?
> >>Thank you!
> >>Tatjana
> >>_______________________________________________
> >>slicer-users mailing list
> >>slicer-users at bwh.harvard.edu
> >>http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> >>To unsubscribe: send email to slicer-users-request at massmail.spl.harvard.edu with unsubscribe as the subject
> >>
> >
> >
> > 
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