Bruker conversion: wrong source for the dimensions

[matthieu....@gmail.com]

Hi!

I am working on a volume acquired into the Bruker data format (http://imaging.mrc-cbu.cam.ac.uk/imaging/FormatBruker), and I opened a 2dseq file.

At first, I noticed the problem mentionned at http://dsi-studio.labsolver.org/discussion-group#!topic/dsi-studio/mspVm7GF5aA and corrected it by modifying the voxel_size(3) value within MATLAB/Octave.

However, it seems that it's not the only problem, because the two other set values correspond to the acquisition resolution, whereas I am working on reconstructed 3D images, with a different reconstruction resolution. The documentation actually mentions at http://dsi-studio.labsolver.org/Manual/Parse-DICOM#TOC-Read-Bruker-2dseq-files that it uses the last one from the "reco" file, but the values do not match:

• Field ##$PVM_SpatResol=( 3 )¶ 0.104 0.104 0.470588235294118 in the Bruker “method” file
  
• Acquisition resolution of (0.104,0.104,0.471) in millimeters using a matrix of 192*96*34 elements (from ##$PVM_Matrix=( 3 )¶ 192 96 34)
  
• Fields ##$RECO_fov=( 3 )¶ 1.9968 0.9984 1.6 and ##$RECO_size=( 3 )¶ 256 128 64 in the Bruker “reco” file
  
• Reconstruction resolution of $RECO_fov / $RECO_size = (0.078,0.078,0.250) in millimeters with a volume of 256*128*64 voxels
  

So it seems that the relevant information is not read from the right file.

Have a nice day,

Matthieu

[Fang-Cheng Yeh]

Hi  Matthieu,

    The latest version should use RECO parameters. You may update DSI Studio and give it a try to see if it works.

    If not, please let me know

Best regards,

Frank

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[Matthieu C]

Hi again Frank,

You were right, thank you for your help!

Best regards,

Matthieu

Le jeudi 5 décembre 2019 16:12:34 UTC+1, Frank Yeh a écrit :

Hi  Matthieu,

    The latest version should use RECO parameters. You may update DSI Studio and give it a try to see if it works.

    If not, please let me know

Best regards,

Frank

On Thu, Dec 5, 2019 at 8:54 AM <matthieu...@gmail.com> wrote:

Hi!

I am working on a volume acquired into the Bruker data format (http://imaging.mrc-cbu.cam.ac.uk/imaging/FormatBruker), and I opened a 2dseq file.

At first, I noticed the problem mentionned at http://dsi-studio.labsolver.org/discussion-group#!topic/dsi-studio/mspVm7GF5aA and corrected it by modifying the voxel_size(3) value within MATLAB/Octave.

However, it seems that it's not the only problem, because the two other set values correspond to the acquisition resolution, whereas I am working on reconstructed 3D images, with a different reconstruction resolution. The documentation actually mentions at http://dsi-studio.labsolver.org/Manual/Parse-DICOM#TOC-Read-Bruker-2dseq-files that it uses the last one from the "reco" file, but the values do not match:

• Field ##$PVM_SpatResol=( 3 )¶ 0.104 0.104 0.470588235294118 in the Bruker “method” file
  
• Acquisition resolution of (0.104,0.104,0.471) in millimeters using a matrix of 192*96*34 elements (from ##$PVM_Matrix=( 3 )¶ 192 96 34)
  
• Fields ##$RECO_fov=( 3 )¶ 1.9968 0.9984 1.6 and ##$RECO_size=( 3 )¶ 256 128 64 in the Bruker “reco” file
  
• Reconstruction resolution of $RECO_fov / $RECO_size = (0.078,0.078,0.250) in millimeters with a volume of 256*128*64 voxels
  

So it seems that the relevant information is not read from the right file.

Have a nice day,

Matthieu

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