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|| ["mri_convert"] || (to convert input volumes to mgh format) || || || ["mri_synthesize"] || (to use the T1 and PD maps to create synthetic images)|| || |
|| [[mri_convert]] || (to convert input volumes to mgh format) || || || [[mri_synthesize]] || (to use the T1 and PD maps to create synthetic images)|| || |
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 anlgle1 |
Volume must be in mgh format |
volume2 |
3D FLASH flip anlgle2 |
Volume must be in mgh format |
output directory |
Where T1 and PD maps are written |
|
Required Flagged Arguments
None
Optional Flagged Arguments
-tr |
Repetition time (ms) |
|
-te |
Echo time (ms) |
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-fa |
Flip angle (degrees) |
|
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) |
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(to use the T1 and PD maps to create synthetic images) |
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Links
Methods Description
N/A
References
None
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>