Numerical Fibre Generator (NFG) Releases

NFG nfg_1.1.1

tclose@stage.nitrcce.org (Tom Close) — Wed, 02 Feb 2011 0:16:00 GMT

Removed unused 'save_combined_mask' option from draw_rois_param.txt (all masks are saved in combined format now) and added code to print header line in 'rois_info.txt' (used to interpret the number codes produced by the 'draw_rois' command).

NeuroImage 2009 Phantoms_A_to_I

tclose@stage.nitrcce.org (Tom Close) — Thu, 01 Apr 2010 5:54:00 GMT

This release contains the 9 phantoms that were used in my 2009 NeuroImage paper on the NFG software, "Close, T. G. Tournier, J-D. Calamante, F. Johnston, L. A. Mareels, I and Connelly, A. 2009. 'A software tool to generate simulated white matter structures for the assessment of fibre-tracking algorithms'. NeuroImage, 47, p1288-1300.".

Phantoms A to D are generated with the default parameters and correspond to phantoms 01 to 04 in the Pre-Generated Phantoms package. However, phantoms E to I are generated with various parameters to demonstrate the range of characteristics that can be produced by the software.

NFG nfg_1.1

tclose@stage.nitrcce.org (Tom Close) — Wed, 29 Apr 2009 6:20:00 GMT

Version 1.1 brings the NFG release inline with the software used in the upcoming manuscript "Close, TG. A Software Tool to generate simulated white matter structures fo rthe assessment of fibre-tracking algorithms, NeuroImage (2009), doi:10.1016/j.neuroimage.2009.03.077."

It adds functionality to automatically draw ROIs around the endpoints of the generated bundles.

It also allows the specification of fixed spherical regions that will repel strands in the optimisation stages. These exclusions are assigned isotropic diffusion characteristics and can be used to model any isotropic substance such as grey matter or CSF.

Pre-Generated Phantoms default_10_v1.0.3

tclose@stage.nitrcce.org (Tom Close) — Sun, 09 Nov 2008 23:25:00 GMT

This release uses the updated mri simulation code in the software version 1.0.3. The structures remain the same as 'default_10_v1.0.1' however the noisy images now have a suitable level of noise and problems with the tensor models used to generate the signal have been fixed.

NFG nfg_1.0.3

tclose@stage.nitrcce.org (Tom Close) — Fri, 07 Nov 2008 6:32:00 GMT

This release fixes persistent bugs with the calculation of the tensor used to generate the signal. The calculated tensors were previously not aligned correctly with the plotted orientations.

NFG nfg_v1.0.2

tclose@stage.nitrcce.org (Tom Close) — Thu, 06 Nov 2008 1:30:00 GMT

This release fixes a bug that effects the orientation of the diffusion tensors used to generate the signal in 'mri_sim'. There was a bug with the elevation angle (into the z orientation) that caused the diffusion tensor to be slightly off line.

NFG nfg_1.0.1

tclose@stage.nitrcce.org (Tom Close) — Thu, 30 Oct 2008 5:23:00 GMT

This update fixes issues with the way noise is added to the images. In the previous version, the default noise_level (0.06) was added to the clean images assuming their intensities were standardised to 1. However, using the default parameters in v1.0 and below, the intensity in the b=0 images is 8000, causing the added noise to be 8000 times to low. This has been fixed in this release by standardising the clean images to 1. To add noise to previously generated images please scale the noise to an appropriate level (i.e. noise_level = 480).

There is also an issue in v1.0 and below when noise is added to small datasets. In this case, images simulated from consecutive gradient directions may end up with the same noise realisation as the random number generator is seeded by the CPU clock at the start of each image and the process may run faster than the time it takes to iterate the clock. This has been fixed by only seeding the random number generator only once at the start of the 'noisify' tool.

Pre-Generated Phantoms default_10_v1.0.1

tclose@stage.nitrcce.org (Tom Close) — Thu, 30 Oct 2008 4:49:00 GMT

This version fixes issues with the noisy images inline with changes made in v1.0.1 of the software. The default 'noise level' (standard deviation of Rician noise) in v1.0 was 4 orders of magnitude too low as it was added assuming that the b=0 images in the clean data set were normalised to 1 (in reality they were 8000). In addition, consecutive gradient direction images may have received the same noise realisation as the noise was seeded of the CPU clock for every direction and it may not have had time to iterate between each gradient direction. This has now been fixed

NFG nfg_1.0

tclose@stage.nitrcce.org (Tom Close) — Thu, 23 Oct 2008 2:00:00 GMT

This is the first full version of the software, including significant bug fixes from version 0.9.5. It is the software used to generate the results in the upcoming paper on the method.

Pre-Generated Phantoms default_10_v1.0

tclose@stage.nitrcce.org (Tom Close) — Thu, 23 Oct 2008 3:03:00 GMT

This release contains 10 example phantoms plus corresponding noisy and noiseless simulated DW-MR images (60 gradient directions SNR=17) generated by NFG v1.0. For variations please download the full software package.