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'''Index''' <<TableOfContents>> |
'''Index''' <<TableOfContents>> |
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|| 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 || |
||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 || |
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|| -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 || ??? || |
||-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 ||??? || |
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|| 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) || |
||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) || |
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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. |
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. |
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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). |
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). |
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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) || || |
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| FreeSurfer | FreeSurfer |
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| Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> | Report bugs to < analysis-bugs@nmr.mgh.harvard.edu > |
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) |
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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 >