Index

Name

mri_ms_fitparms - Estimates tissue parameter maps (T1, proton density) from multi-spectral FLASH MRI

Synopsis

mri_ms_fitparms [options] <volume1> <volume2> ... <output directory>

Arguments

Positional Arguments

volume1

3D FLASH flip angle1

Volume must be in mgh format

volume2

3D FLASH flip angle2

Volume must be in mgh format

output directory

Where T1 and PD maps are written

Required Flagged Arguments

None

Optional Flagged Arguments

-afi, -fam

Designate flip angle map, we assume that the nominal flip angle is 60 degrees if B1 was homogeneous <also assumes that the afi map is registered to the flash volumes>

-ait

Apply inverse of transform

-at

Set acquisition time

-conform

Interpolate volume to be isotropic 1mm^3

-correct

Correct proton density map (PD) by T2* estimates

-cubic

Use cubic interpolation

-dt

Numerical integration time step used to estimate the flip angle field from multiple acquisitions of different flip angles and/or TRs

-fa

Flip angle (degrees)

-fa_scale

Set value to scale all flip angles by

-faf

Designate flip angle map to use with specified control points

-fsmooth

Smooth flip angle map for X iterations of soap bubble smoothing (thres=??)

-i

Invert

-m

Set momentum

-max

Set max T2*

-n

Perform estimation/motion correction X times (-n 0 runs without motion correction)

-nearest

Use nearest-neighbor interpolation

-nocompress

Do not compress output volumes (save as .mgh)

-nosynth

Disable volume synthesis

-r

write out residuals to designated location

-s

Smooth faf field with sigma=X

-scale

Scale volumes by X after reading

-sinc

Use sinc interpolation (default window width is 6)

-t

Apply transform to output volumes

-te

Echo time (ms)

-tr

Repetition time (ms)

-trilinear

Use trilinear interpolation

-tukey

Use tukey bi-weight of residuals

-u

???

-use_brain_mask

Compute a brain mask from the PD map and use it when computing registration

-w

Write out intermediate results every X iterations

-window

???

Outputs

T1.mgz

Compressed T1 map

PD.mgz

Compressed Proton Density map

vol0.mgz

Compressed Synthetic volume for input <volume1>, in motion corrected space

vol0.lta

Motion correction afine information (text file)

vol1.mgz

Compressed Synthetic volume for input <volume2>, in motion corrected space

vol1.lta

Motion correction afine information (text file)

Description

This program takes an arbitrary # of FLASH images as input, and estimates the T1 and PD values of the data for voxel, as well as a linear transform aligning each of the images. The T1 and PD maps are written into <output directory> together with synthetic volumes names vol?.mgh, one for each of the input volumes. All the output volumes are generated in the common (motion-corrected) space. Note that TR, TE and the flip angle are read directly from the image header. If this information is not available, it can be specified on the command line using -tr <TR in msec> -te <TE in msec> -fa <flip angle in degrees> before each volume.

Examples

Example 1

cd subjectid/mri/flash

mri_ms_fitparms -tr 20 -te 6 -fa 5 flash5.mgh -tr 20 -te 6 -fa 30 flash30.mgh .

Description: Two 3D FLASH volumes (flip angles 5 and 30 degrees), both acquired with the same TE (20ms) and TR (6ms) are used to fit T1 and PD map and write the results on the same directory (subjectid/mri/flash).

Bugs

None

See Also

mri_convert

(to convert input volumes to mgh format)

mri_synthesize

(to use the T1 and PD maps to create synthetic images)

Links

FreeSurfer

Methods Description

N/A

References

None

Reporting Bugs

Report bugs to < analysis-bugs@nmr.mgh.harvard.edu >

Author/s

BruceFischl

mri_ms_fitparms (last edited 2015-05-29 11:20:17 by AllisonMoreau)