can't read an nrrd header

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can't read an nrrd header

Murat Maga

Hi All,

 

I have a raw image I am trying to get into the Slicer. Below is the header that describes the data.

 

NRRD0004

space: 3D-right-handed

type: unsigned char

dimension: 3

sizes: 512 512 454

spacings: 1 1 1

encoding: raw

data file: ./824-L1.gray

 

I am constantly getting this error:

 

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\..\Slicer4\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx, line 316

vtkMRMLVolumeArchetypeStorageNode (000000001A6B6FA0): ReadData: Cannot read file, fullName = C:/temp/824-L1.pvl.nc.nrrd, number of files listed in the node = 0, the ITK reader says it was able to read 1 files, the reader used the archetype file name of C:/temp/824-L1.pvl.nc.nrrd

ERROR: In ..\..\..\..\..\Slicer4\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx, line 319

vtkMRMLVolumeArchetypeStorageNode (000000001A6B6FA0): reader 0th file name = C:/temp/824-L1.pvl.nc.nrrd

 

 

If I remove the “Space:” field it works, but then my images are mirrored.

 

What am I doing wrong?

 

M


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Re: can't read an nrrd header

Julien Finet
Hi,

I'm not too familiar with nrrd. But here is the full doc:
It is mentioned that it's better to have no spacing field than having a spacing of 1 1 1. 

If you have your image mirrored, you can probably play with the space: values. Change from 3D right handed to  3D-left-handed .

j.

On Tue, Apr 17, 2012 at 5:00 PM, Murat Maga <[hidden email]> wrote:

Hi All,

 

I have a raw image I am trying to get into the Slicer. Below is the header that describes the data.

 

NRRD0004

space: 3D-right-handed

type: unsigned char

dimension: 3

sizes: 512 512 454

spacings: 1 1 1

encoding: raw

data file: ./824-L1.gray

 

I am constantly getting this error:

 

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\..\Slicer4\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx, line 316

vtkMRMLVolumeArchetypeStorageNode (000000001A6B6FA0): ReadData: Cannot read file, fullName = C:/temp/824-L1.pvl.nc.nrrd, number of files listed in the node = 0, the ITK reader says it was able to read 1 files, the reader used the archetype file name of C:/temp/824-L1.pvl.nc.nrrd

ERROR: In ..\..\..\..\..\Slicer4\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx, line 319

vtkMRMLVolumeArchetypeStorageNode (000000001A6B6FA0): reader 0th file name = C:/temp/824-L1.pvl.nc.nrrd

 

 

If I remove the “Space:” field it works, but then my images are mirrored.

 

What am I doing wrong?

 

M


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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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Re: can't read an nrrd header

Murat Maga
In reply to this post by Murat Maga

Hi,

 

I found that replacing “spacings: 1 1 1” with “space directions: (1,0,0) (0,1,0) (0,0,1)” fixes the error. Now I have a separate issue.

 

When imported this way, 3D rendering of the specimen is correct (i.e. it is not mirrored). However, the cross-section shown in “Red” window is mirrored. Yet, when I record the 3D coordinate of an anatomical landmark, it has correct voxel coordinates. “Correct” in both cases mean, that it is identical to the coordinates and 3D renderings created by the scanner vendor’s software.

 

Any suggestions how I can fix this.

 

Best,

M

 

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Murat Maga
Sent: Tuesday, April 17, 2012 2:01 PM
To: [hidden email]
Subject: [slicer-users] can't read an nrrd header

 

Hi All,

 

I have a raw image I am trying to get into the Slicer. Below is the header that describes the data.

 

NRRD0004

space: 3D-right-handed

type: unsigned char

dimension: 3

sizes: 512 512 454

spacings: 1 1 1

encoding: raw

data file: ./824-L1.gray

 

I am constantly getting this error:

 

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\..\Slicer4\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx, line 316

vtkMRMLVolumeArchetypeStorageNode (000000001A6B6FA0): ReadData: Cannot read file, fullName = C:/temp/824-L1.pvl.nc.nrrd, number of files listed in the node = 0, the ITK reader says it was able to read 1 files, the reader used the archetype file name of C:/temp/824-L1.pvl.nc.nrrd

ERROR: In ..\..\..\..\..\Slicer4\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx, line 319

vtkMRMLVolumeArchetypeStorageNode (000000001A6B6FA0): reader 0th file name = C:/temp/824-L1.pvl.nc.nrrd

 

 

If I remove the “Space:” field it works, but then my images are mirrored.

 

What am I doing wrong?

 

M


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slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: can't read an nrrd header

Murat Maga
In reply to this post by Julien Finet

Hi Julien,

 

Yes I tried the 3d-left-handed, but then I receive this error:

 

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 261

vtkNRRDReader (0000000017A39ED0): Error reading C:/temp/801-L2_ras.nrrd: [nrrd] nrrdLoad: trouble reading "C:/temp/801-L2_ras.nrrd"

[nrrd] nrrdRead: trouble

[nrrd] _nrrdRead: trouble reading NRRD file

[nrrd] _nrrdFormatNRRD_read: trouble parsing space info "3d-left-handed"

[nrrd] _nrrdReadNrrdParse_space: couldn't parse space "3d-left-handed"

 

 

Everything else (3d-right-handed, ras, scanner-xyz) seems to work. Is this a bug in the nrredread function?

 

M

 

From: Julien Finet [mailto:[hidden email]]
Sent: Tuesday, April 17, 2012 3:27 PM
To: Murat Maga
Cc: [hidden email]
Subject: Re: [slicer-users] can't read an nrrd header

 

Hi,

 

I'm not too familiar with nrrd. But here is the full doc:

It is mentioned that it's better to have no spacing field than having a spacing of 1 1 1. 

 

If you have your image mirrored, you can probably play with the space: values. Change from 3D right handed to  3D-left-handed .

j.

On Tue, Apr 17, 2012 at 5:00 PM, Murat Maga <[hidden email]> wrote:

Hi All,

 

I have a raw image I am trying to get into the Slicer. Below is the header that describes the data.

 

NRRD0004

space: 3D-right-handed

type: unsigned char

dimension: 3

sizes: 512 512 454

spacings: 1 1 1

encoding: raw

data file: ./824-L1.gray

 

I am constantly getting this error:

 

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\..\Slicer4\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx, line 316

vtkMRMLVolumeArchetypeStorageNode (000000001A6B6FA0): ReadData: Cannot read file, fullName = C:/temp/824-L1.pvl.nc.nrrd, number of files listed in the node = 0, the ITK reader says it was able to read 1 files, the reader used the archetype file name of C:/temp/824-L1.pvl.nc.nrrd

ERROR: In ..\..\..\..\..\Slicer4\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx, line 319

vtkMRMLVolumeArchetypeStorageNode (000000001A6B6FA0): reader 0th file name = C:/temp/824-L1.pvl.nc.nrrd

 

 

If I remove the “Space:” field it works, but then my images are mirrored.

 

What am I doing wrong?

 

M


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slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject

 


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Re: can't read an nrrd header

Julien Finet
Sorry I'm not sure I can help.

You might want to contact the VTK mailing list or the teem mailing list:

https://lists.sourceforge.net/lists/listinfo/teem-users

j.

On Wed, Apr 18, 2012 at 2:42 PM, Murat Maga <[hidden email]> wrote:

Hi Julien,

 

Yes I tried the 3d-left-handed, but then I receive this error:

 

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 261

vtkNRRDReader (0000000017A39ED0): Error reading C:/temp/801-L2_ras.nrrd: [nrrd] nrrdLoad: trouble reading "C:/temp/801-L2_ras.nrrd"

[nrrd] nrrdRead: trouble

[nrrd] _nrrdRead: trouble reading NRRD file

[nrrd] _nrrdFormatNRRD_read: trouble parsing space info "3d-left-handed"

[nrrd] _nrrdReadNrrdParse_space: couldn't parse space "3d-left-handed"

 

 

Everything else (3d-right-handed, ras, scanner-xyz) seems to work. Is this a bug in the nrredread function?

 

M

 

From: Julien Finet [mailto:[hidden email]]
Sent: Tuesday, April 17, 2012 3:27 PM
To: Murat Maga
Cc: [hidden email]
Subject: Re: [slicer-users] can't read an nrrd header

 

Hi,

 

I'm not too familiar with nrrd. But here is the full doc:

It is mentioned that it's better to have no spacing field than having a spacing of 1 1 1. 

 

If you have your image mirrored, you can probably play with the space: values. Change from 3D right handed to  3D-left-handed .

j.

On Tue, Apr 17, 2012 at 5:00 PM, Murat Maga <[hidden email]> wrote:

Hi All,

 

I have a raw image I am trying to get into the Slicer. Below is the header that describes the data.

 

NRRD0004

space: 3D-right-handed

type: unsigned char

dimension: 3

sizes: 512 512 454

spacings: 1 1 1

encoding: raw

data file: ./824-L1.gray

 

I am constantly getting this error:

 

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\Slicer4\Libs\vtkTeem\vtkNRRDReader.cxx, line 511

vtkNRRDReader (000000000C1ED6D0): ReadImageInformation: Error interpreting nrrd spacing (nrrdSpacingStatusScalarWithSpace)

ERROR: In ..\..\..\..\..\Slicer4\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx, line 316

vtkMRMLVolumeArchetypeStorageNode (000000001A6B6FA0): ReadData: Cannot read file, fullName = C:/temp/824-L1.pvl.nc.nrrd, number of files listed in the node = 0, the ITK reader says it was able to read 1 files, the reader used the archetype file name of C:/temp/824-L1.pvl.nc.nrrd

ERROR: In ..\..\..\..\..\Slicer4\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx, line 319

vtkMRMLVolumeArchetypeStorageNode (000000001A6B6FA0): reader 0th file name = C:/temp/824-L1.pvl.nc.nrrd

 

 

If I remove the “Space:” field it works, but then my images are mirrored.

 

What am I doing wrong?

 

M


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject

 


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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject