Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

This website has been deprecated and exists as an archive only.

The TORTOISE website has been moved to https://tortoise.nibib.nih.gov.

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

Version Update Notes

Updates to TORTOISE Version 2.0.2

Updates to DIFF_CALC

  1. Several bug fixes.

Updates to DIFF_PREP

Several minor changes:

  1. The resolution problem with monitors less than 720p have been fixed.
  2. Several other bug fixes, performance improvements.
  3. Cubic eddy correction included.
  4. Optimization settings for predefined sets have been made available in DIFFPREP_GUI.

Updates to TORTOISE Version 2.0.1

Updates to DIFF_CALC

  1. The Export tool for AFNI exports the correct gradient information now.

Updates to DIFF_PREP

Several minor changes:

  1. Tooltips added to DIFFPREP GUI. When the mouse is pointed over a button, additional information is displayed.
  2. Several GUI labels are changed to more user-friendly versions.

Updates to TORTOISE Version 2.0.0

Updates to DIFF_CALC

DIFF_CALC improvements were mostly minor improvements and bug fixes.

  1. Bug fixes for using external masks.
  2. Right-Left orientation in DTITK export module made consistent with DTITK's qform norms. Data from previous versions were horizontally flipped during DTITK correction. Tensors exported with this version will not be.

Updates to DIFF_PREP

There were several major and minor improvements to DIFF_PREP.

Minor improvements:

  1. Several minor bug fixes for the processing module and import modules.
  2. PAR/REC import routine changed to output the "Display value" instead of "floating point value."
  3. A phase encoding option added for NIFTI import. While importing NIFTI files, users can now select the direction of the phase encoding.
  4. "Reslice nii" option is faster and does not change images' matrix sizes anymore.
  5. A new option to change the orientation of the imported images added. This "Original Image Axis for flipping" can change the axes of the original image to whichever orientation the user needs. The B-matrix is rotated accordingly. The orientation convention of DIFF_PREP is as follows:
    • The (0,0,0) coordinate of the image is the bottom left of the image (instead of top left as in ITK convention). The standard orientation is from left of the image to right: right to left anatomical, bottom to top of the image is posterior-anterior anatomical, increasing slice number is superior. Therefore in our standard orientation convention, our framework is 'LAS'.
    • With this new reorientation tool, the users can provide the original orientation of the image (for example 'ASL' for sagittal) and the images and the B-matrix will be transposed to DIFF_PREP's standard convention, 'LAS'.
  6. A new checkbox is added to enable and disable the "registration progression windows". Default is enabled and the log windows and the image windows are displayed. When disabled no GUI related windows are created. This may be useful for users willing to batch process their data.
  7. The users can now limit the CPU usage of DIFF_PREP by creating a text file in their DIFF_PREP_WORK directory in their home folder. This file should be named "NCPUs.cfg" and contain one line, indicating the number of cores DIFF_PREP is allowed to use. If this file does not exist or if it contains "0", all available cores will be used.

New features:

  1. Parallel processing capabilities. If the user has a valid IDL license and runs DIFF_PREP from IDL command line instead of the provided virtual machine, the software will use all CPU cores for correction. It will perform each DWI-to-b0 image correction using a different core by creating separate IDL threads. The number of threads created is the maximum of number of cores in the system or 16. For example, if the system has 8 cores (hyper-threaded included) and 15 volumes, all 8 cores will be used for the first 8 DWI volumes and then 7 cores will be used for the last 7 volumes.
    Unfortunately, this feature is only available to users with an IDL license and not in virtual machine. The reason is because of limitations of the IDL language for virtual machine users. Additionally, the IDL_IDLBRIDGE object that we employ for multi-threading is known to contain bugs. BECAUSE OF THESE BUGS, WE STRONGLY SUGGEST TO PERFORM ONLY 1 DIFF_PREP RUN AT A TIME WITH PARALLEL PROCESSING ENABLED. Unexpected results or crashes might occur if more than 16 IDL threads(limit of DIFF_PREP thread count) are created with a single computer even if the runs are independent.
  2. Cubic correction for eddy-currents distortions. DIFF_PREP employs the solutions to the Laplace equation in Cartesian coordinates to correct for eddy-currents distortions. Basis functions upto and including the quadratic terms have been the transformations employed by DIFF_PREP. However, recently we encountered several datasets that required even higher order terms and now we are providing the option to use "cubic terms" for eddy current corrections. This option is by default disabled but if the user would like to enable it, he/she can manually edit the "settings_mecc3d.xml" file in TORTOISE_installation_folder/DIFF_PREP/diffprep_main/software/settings. Changing the last seven zeros in the "<opt_par>" XML tag to 1 will enable cubic correction.
  3. Blip-up blip-down EPI distortion correction tool. A new tool is provided to correct for EPI distortions when duplicate versions of the same data is acquired with reversed phase encoding directions. This tool is still in alpha phase. The corresponding academic paper is currently being written. The usage instructions can be found at: bup_bdown_wiki_details.pdf (PDF, 162KB)

Updates to TORTOISE Version 1.4.0

Updates to DIFF_PREP

DIFF_PREP improvements were mostly about data import.

  1. Bruker import improved. Problems with 3D EPI scans are fixed.
  2. FSL NIFTI import improved.
  3. Philips DICOM import made more robust.
  4. Siemens Mosaic DICOM import significantly improved. Image and slab sizes and dimensions are now checked with two different methods and if the two methods do not agree a warning message is displayed to warn users for possible contingencies.
  5. The bug that caused the default "Flip Y" setting to remain off when Siemens Mosaic import function is used, is fixed.
  6. Optimized parameters for using DIFF_PREP for distortion corrections on rat brain are available. Contact us for more details if you are working with rats, or other small sized animals/objects.
  7. Several performance enhancements were implemented.

Updates to DIFF_CALC

  1. New masking options are added to DIFF_CALC. These can be found in the "Opt" part of the "mask raw images" button. The users are now able to directly load an external mask, in NIFTI or ANALYZE format, save the current mask, or repeatedly load different mask images to either combine them (logical OR) or remove unwanted regions (logical NOT).
  2. Triplanar linefield visualization problems fixed. Now this visualization works correctly when data acquisition is different than axial, i.e. coronal or sagittal.
  3. DTITK tensors can correctly be imported into TORTOISE .list file format. Please ignore the error messages during this process, and make sure to "Compute eigenvalues", "Derive Variables" and "Save Session" after the import process.

Updates to TORTOISE Version 1.3.0

Phantom Analysis - A new utility included in TORTOISE

This utility is for analysis of multi-center diffusion tensor phantom data, as described in Walker, L., et. al., A framework for the analysis of phantom data in multicenter diffusion tensor imaging studies. Hum Brain Mapp. 34(10):2439-54.

The user provides a list of co-registered tensor derived metrics (i.e. FA, TR, etc), and the utility computes 1) the difference of each input image from the median of all images, and 2) the inter- and intra-site variance, variability and ICCs.

Updates to DIFF_PREP

  1. Bruker import improved. Problems with repeats and averages fixed.
  2. A bug in PAR/REC import fixed, and routine made more robust.
  3. In Siemens Mosaic import, the user can now input the number of images in a single row of the mosaic. Occasionally, the needed information to automatically “chop” up the mosaic into individual axial slices fails. Providing this input will correct this problem.
  4. Jacobian modulation for EPI correction and noise estimation is no longer being applied. This modulation is still being applied for Eddy current distortion correction.
  5. Additional new import options include:
    • Flip slice order: TORTOISE assumes a frame of reference in which datasets are acquired inferior to superior (i.e. first slice is closer to the cerebellum, while last slice is closer to the top of the skull). If data is acquired in the superior-to-inferior slice order, this option should be used. Note: this was previously available, but contained a few bugs that have been fixed.
    • Reslice NII for FSL nifti import: by default, TORTOISE uses transformation information contained in the nifti header. If, after import, the user finds that their data is not oriented as desired, this option can be turned off.
    • Swap gradients: the user is given the option to swap x and y, x and z, or y and z gradients (i.e. swapping the columns of the gradient table). TORTOISE assumes that the gradient vectors are in the order of read, phase, slice. This may not be correct if, for example, a left-right phase encoding is used for axial DTI acquisitions. In that case, the x and y gradients (read and phase) may need to be swapped.
  6. We now support Philips DICOM format.
  7. Similar to the Reslice NII for nifti import, there is a Reslice NII option for the structural image. If the nifti header contains a transformation that the user DOES NOT wish to apply, then this option should be turned off. Due to reference frame conventions, this will often result in the structural image being flipped in the Anterior Posterior (AP) direction. See number 8 below on fixing this.
  8. If the user finds that their structural image is being flipping in the AP direction, then the option to flip AP is now available to the user.
    • Important Note: If the user needs to play around with the Reslice NII and flip AP options, we HIGHLY RECOMMEND that the user double checks that there has not been any un-wanted flipping in the Left-Right direction. This can be done by visually comparing a non-diffusion weighted (b0) image and your structural target image for mirror symmetry. Take a look particularly at the ventricles, which are often asymmetric between hemispheres. If you have already run your data through diffprep, then this can be compared using …_b0_orig_crop.nii and … _rpd_structural.nii, which should both be in your _proc directory. If your structural target is flipped Left/Right compared to the b0 image, then you should use image software, such as MIPAV, to flip your structural target image Left/Right to match the diffusion data.
  9. Optimized parameters for using DIFF_PREP for distortion corrections on rat brain are available. Contact us for more details if you are working with rats, or other small sized animals/objects.

Updates to DIFF_CALC

  1. Fixes to issues which caused the software to crash with Mac OS X Lion (10.7).
  2. Updates to the GUI of the tensor fitting options menu.
  3. Automatic noise estimation using robust methods now provides the option to enter the fraction of datapoints that the user would like to be considered as outliers. Default value is 0.05 (i.e. 5%), which is conservative. With 30 directions, 10% gives reasonable results, in our experience.

Please report any issues, errors, etc, to tortoisedti@gmail.com. If you encounter difficulties in importing your raw data, please let us know, as we are continuing to improve those routines.