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For any information about TORTOISE generation V3.x.x, please refer to the new website.

Data Import

We have modules for importing Philips PAR/REC, Philips DICOM,GE DICOM, SIEMENS DICOM, SIEMENS MOSAIC DICOM and FSL 4D NIFTI as part of DIFF_PREP. Please see the Data Importing page of the software guide for detailed instructions on importing your data.

Data must be imported to a format which our software can read. This is a very simple format consisting of three text files: a header file (.list), a file of pointers to the raw data (.path) and a b-matrix file (.bmtxt). These are described in more detail in the data format section of the Software Guide for DIFF_PREP.

The most important step in importing your data is having or creating a correct gradient file. This should be a plain text file with tab or space separated values (note: this file must be saved as plain text and not as rich text format). The first line must contain the number of volumes in your DTI data set, and all subsequent lines contain 3 columns with the 3 gradient vector values in the order x y z. There must be 1 row of values for each volume of your DTI data set. If you use multiple b-values in your acquisition, the gradient vectors must be scaled down according to the b-value as described in Mattiello, et al¹. The sample gradient file below contains 6 directions plus 1 b0, repeated 4 times at b = 1000s/mm², and 2 times at b = 500s/mm² for a total of 42 volumes. The b500 volumes were acquired in the middle, with 2 b1000 sets before and after.

42
      0.00000      0.00000      0.00000
     0.707107      0.00000     0.707107
    -0.707107      0.00000     0.707107
      0.00000     0.707107     0.707107
      0.00000     0.707107    -0.707107
     0.707107     0.707107      0.00000
    -0.707107     0.707107      0.00000
      0.00000      0.00000      0.00000
     0.707107      0.00000     0.707107
    -0.707107      0.00000     0.707107
      0.00000     0.707107     0.707107
      0.00000     0.707107    -0.707107
     0.707107     0.707107      0.00000
    -0.707107     0.707107      0.00000
      0.00000      0.00000      0.00000
     0.500000      0.00000     0.500000
    -0.500000      0.00000     0.500000
      0.00000     0.500000     0.500000
      0.00000     0.500000    -0.500000
     0.500000     0.500000      0.00000
    -0.500000     0.500000      0.00000
      0.00000      0.00000      0.00000
     0.500000      0.00000     0.500000
    -0.500000      0.00000     0.500000
      0.00000     0.500000     0.500000
      0.00000     0.500000    -0.500000
     0.500000     0.500000      0.00000
    -0.500000     0.500000      0.00000
      0.00000      0.00000      0.00000
     0.707107      0.00000     0.707107
    -0.707107      0.00000     0.707107
      0.00000     0.707107     0.707107
      0.00000     0.707107    -0.707107
     0.707107     0.707107      0.00000
    -0.707107     0.707107      0.00000
      0.00000      0.00000      0.00000
     0.707107      0.00000     0.707107
    -0.707107      0.00000     0.707107
      0.00000     0.707107     0.707107
      0.00000     0.707107    -0.707107
     0.707107     0.707107      0.00000
    -0.707107     0.707107      0.00000

If you find that the bmatrix is incorrect for your data (see Loading, viewing and inital QC), then try to use the "Flip" radio buttons in the import module to adjust your gradient file appropriately.

If you have data in another format other than those listed above, you can manually create your .list, .path and .bmtxt files, according to the descriptions in the above listed pages. Supported raw data formats are: integer, float, and dicom.

We hope to include support for raw DWI data in analyze format and Philips dicom in a future release.

References

Mattiello, J., Basser, P.J., and LeBihan, D. (1997) The b matrix in diffusion tensor echo-planer imaging. Magn Reson Med. 37:292–300. PMID:9001155