Index
Contents
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
(to convert input volumes to mgh format) |
|
|
(to use the T1 and PD maps to create synthetic images) |
|
Links
Methods Description
N/A
References
None
Reporting Bugs
Report bugs to < analysis-bugs@nmr.mgh.harvard.edu >