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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

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)

-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

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)