Difference between revisions of "NAMIC"

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m (Update from Wiki)
m (Update from Wiki)
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Note: please also see [[NAMIC-Dartmouth-DWI|this page about NRRD headers which refer to the original image files]], without the need for any additional data reading with MATLAB.
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Please refer to the [[NAMIC_Wiki:DTI:Nrrd_format|NRRD header spec]] to interpret these header files.
  
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The following MATLAB script converts the Dartmouth DWIs into a single file in which the volumes (2 baselines and 12 diffusion weighted images) are in the appropriate space. The resulting raw image, together with [[NAMIC-Dartmouth-nrrdheader|a nrrd header]], are used by Slicer to do DTI analysis.
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The NRRD headers here do not require any additional data processing or manipulation, and thus represent an alternative to the [[NAMIC-Dartmouth-DWI-to-NRRD-Format|NRRD headers based on a MATLAB script]]
  
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fpout = fopen('nrrdraw.raw', 'w');
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The tar files on BIRN for the DWI studies of six anonymous controls are:
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  for k = 1:14;
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    % for subject 1,2,4,5 the slice order is Superior-Inferior, need to
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* NAMIC01dti-anon.tgz
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    % reverse order
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* NAMIC02dti-anon.tgz
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    % for m = 36:-1:1
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* NAMIC03dti-anon.tgz
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    % for subject 3, 6, the slice order is Inferior-superior
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* NAMIC04dti-anon.tgz
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    for m = 1:36
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* NAMIC05dti-anon.tgz
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      n = (k-1)*36+m;
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* NAMIC06dti-anon.tgz
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      % use appropriate dicom prefix
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      name = sprintf('S8.%03d', n);
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Un-tarring each file (by <tt>tar xzvf</tt>) creates a <tt>dti-anon</tt> subdirectory (so these <tt>.tgz</tt> files should probably be placed in separate numbered directories).
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      fp = fopen(name);
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      fseek(fp, -65536*2, 'eof');
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The following NRRD headers are to be placed within the <tt>dti-anon</tt> subdirectories, since they refer to the "S" slice image files withn them. The position and orientation information in the NRRD headers was determined from the DICOM tags, and all the scan sequence-specific (b-value and gradients) was copied from the earlier [[NAMIC-Dartmouth-nrrdheader|MATLAB-based NRRD header]].
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      A = fread(fp, [256 256], 'short');
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      fclose(fp);
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* [[NAMIC01-dwi-nhdr|NAMIC01-dwi-nhdr]]
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      fwrite(fpout, A, 'short');
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* [[NAMIC02-dwi-nhdr|NAMIC02-dwi-nhdr]]
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    end
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* [[NAMIC03-dwi-nhdr|NAMIC03-dwi-nhdr]]
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    end
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* [[NAMIC04-dwi-nhdr|NAMIC04-dwi-nhdr]]
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  fclose(fpout);
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* [[NAMIC05-dwi-nhdr|NAMIC05-dwi-nhdr]]
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* [[NAMIC06-dwi-nhdr|NAMIC06-dwi-nhdr]]

Revision as of 13:56, 18 December 2006

Home < NAMIC

Please refer to the NRRD header spec to interpret these header files.

The NRRD headers here do not require any additional data processing or manipulation, and thus represent an alternative to the NRRD headers based on a MATLAB script

The tar files on BIRN for the DWI studies of six anonymous controls are:

  • NAMIC01dti-anon.tgz
  • NAMIC02dti-anon.tgz
  • NAMIC03dti-anon.tgz
  • NAMIC04dti-anon.tgz
  • NAMIC05dti-anon.tgz
  • NAMIC06dti-anon.tgz

Un-tarring each file (by tar xzvf) creates a dti-anon subdirectory (so these .tgz files should probably be placed in separate numbered directories).

The following NRRD headers are to be placed within the dti-anon subdirectories, since they refer to the "S" slice image files withn them. The position and orientation information in the NRRD headers was determined from the DICOM tags, and all the scan sequence-specific (b-value and gradients) was copied from the earlier MATLAB-based NRRD header.

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