Built-In Functions

Jim's Image Fitting has several built-in fit functions for some of the more common fitting procedures. You can set up Image Fitting to perform one of these fits by selecting appropriate tab:

These are the built-in functions:

T2/R2

T₂ or R₂ estimation from MR sequences with different echo times (TE). Enter the TE values in milliseconds. The T₂ will be estimated in milliseconds. This is also used to estimate T₂^* or R₂^* if you have acquired gradient-echo images rather than spin-echo.

Output parameters: M0 and T2 or R2

Select if you want to produce an R₂ parameter map, rather than a T₂ map.

By default, T₂ maps will be created with units of milliseconds, and R₂ maps with units of milliseconds^-1. Select if you want to produce parameter maps with units of seconds or seconds^-1.
Note: be sure to select if either of the above options is selected, since images with integer intensities cannot store the parameter values with sub-integer accuracy.

In order place limits on the large fitted parameter values that can occur due to noise in the images, you may want to enter the maximum physically feasible T₂ value here: . In vivo T₂ values do not normally exceed 3 seconds. The minimum T₂ is automatically limited to zero.

SR T1/R1

Saturation-recovery T₁ or R₁ estimation from MR sequences with different repetition times (TR) (time between the 90° excitation pulses). Enter the TR values in milliseconds. The T₁ will be estimated in milliseconds.

Output parameters: M0 and T1 or R1

Select if you want to produce an R₁ parameter map, rather than a T₁ map.

By default, T₁ maps will be created with units of milliseconds, and R₁ maps with units of milliseconds^-1. Select if you want to produce parameter maps with units of seconds or seconds^-1.
Note: be sure to select if either of the above options is selected, since images with integer intensities cannot store the parameter values with sub-integer accuracy.

You can place limits on the large fitted parameter values that can occur due to noise in the images, by entering the maximum physically feasible T₁. The minimum T₁ is automatically limited to zero.

FLASH T1/R1

T₁ or R₁ estimation from FLASH sequences with different flip angles (alpha). Enter the alpha values in degrees and enter the (constant) TR value (in milliseconds). The T₁ will be estimated in milliseconds.

Output parameters: M0 and T1 or R1

Select if you want to produce an R₁ parameter map, rather than a T₁ map.

By default, T₁ maps will be created with units of milliseconds, and R₁ maps with units of milliseconds^-1. Select if you want to produce parameter maps with units of seconds or seconds^-1.
Note: be sure to select if either of the above options is selected, since images with integer intensities cannot store the parameter values with sub-integer accuracy.

You can place limits on the large fitted parameter values that can occur due to noise in the images, by entering the maximum physically feasible T₁. The minimum T₁ is automatically limited to zero.

MRI scanners may not produce accurate flip angles for their RF pulses, so the flip angles you enter may need to be scaled with a scaling factor that depends on position in the image. This can achieved using a flip angle calibration method, which produces an image of the flip angle scaling factor needed. In regions where the flip angle calibration is correct, the scaling factor image would have a value of 1.0; in regions where the actual flip angle is lower than the nominal value, the scaling factor image would have a value less than 1.0; in regions where the actual flip angle is greater than the nominal value, the scaling factor image would have a value greater than 1.0. If you want to correct the flip angle in this way, select and the select the flip angle calibration image:

IR T1/R1

Inversion-recovery T₁ or R₁ estimation from phase-sensitive or absolute-value MR sequences with different inversion times (TI) (time between the 180° inversion pulse and the excitation pulse). Enter the TI values in milliseconds. The T₁ will be estimated in milliseconds.

Output parameters: M0 and T1 or R1

Select if you want to produce an R₁ parameter map, rather than a T₁ map.

By default, T₁ maps will be created with units of milliseconds, and R₁ maps with units of milliseconds^-1. Select if you want to produce parameter maps with units of seconds or seconds^-1.
Note: be sure to select if either of the above options is selected, since images with integer intensities cannot store the parameter values with sub-integer accuracy.

You can place limits on the large fitted parameter values that can occur due to noise in the images, by entering the maximum physically feasible T₁. The minimum T₁ is automatically limited to zero.

The Fitter can fit to either phase-sensitive IR images (with both positive and negative pixel intensities), or absolute value (magnitude) images. If you are working with magnitude images, select .

MOLLI T1/R1

Modified Look-Locker Inversion-Recovery (MOLLI) T₁ or R₁ estimation from phase-sensitive or absolute-value MR sequences with different inversion times (TI). This is similar to IR T1/R1 above, except that there is an additional fitted parameter (B) to allow for the fact that the longitudinal magnetization is perturbed by the train of read-out pulses. fitting function">

Output parameters: M0, B (scaled by a factor of 1000) and T1 or R1

ADC

Apparent diffusion coefficient (ADC) estimation from diffusion-weighted images with different b-factors. Enter the b-factors in seconds per square millimetre. The ADC will be estimated in microns²/second.

Output parameters: M0 and ADC

You can place limits on the large fitted ADC values that can occur due to noise in the images, by entering the maximum physically feasible ADC value. The minimum ADC is automatically limited to zero.

If you have suggestions for more built-in fitting functions to include, please mail them to .