|
|
Documentation.Diffusivity History
Hide minor edits - Show changes to output
Changed lines 26-28 from:
*'''For Camino users''': In general, it depends on how the scheme file is created. If the scheme file conforms to the default unit of Camino, the diffusivity unit should be m'^2^'.s'^-1^'. In this case, the multiplication factor should be 1e9.
*'''For FSL users''': If the correct b-value is used for the corresponding entries in the bval file, then the diffusivity unit should be mm'^2^'.s'^-1^'. In this case, the multiplication factor should be 1e3. to:
*'''For Camino users''': In general, it depends on how the scheme file is created. If the scheme file conforms to the default unit of Camino, the diffusivity unit should be m'^2^'.s'^-1^'. In this case, the multiplication factor should be 10^9.
*'''For FSL users''': If the correct b-value is used for the corresponding entries in the bval file, then the diffusivity unit should be mm'^2^'.s'^-1^'. In this case, the multiplication factor should be 10^3.
Changed lines 26-28 from:
*'''For Camino users''': In general, it depends on how the scheme file is created. If the scheme file conforms to the default unit of Camino, the diffusivity unit should be m'^2^'.s'^-1^'.
*'''For FSL users''': If the correct b-value is used for the corresponding entries in the bval file, then the diffusivity unit should be mm'^2^'.s'^-1^'. to:
*'''For Camino users''': In general, it depends on how the scheme file is created. If the scheme file conforms to the default unit of Camino, the diffusivity unit should be m'^2^'.s'^-1^'. In this case, the multiplication factor should be 1e9.
*'''For FSL users''': If the correct b-value is used for the corresponding entries in the bval file, then the diffusivity unit should be mm'^2^'.s'^-1^'. In this case, the multiplication factor should be 1e3.
Changed line 8 from:
The unit used by DTI-TK is 10'^-3^'mm'^2^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3. to:
'''The unit used by DTI-TK is''' 10'^-3^'mm'^2^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3.
Changed lines 17-18 from:
Here, you can download the example data set to see what a DTI-TK compatible DTI volume looks like.
to:
Please download the [[http://www.nitrc.org/frs/download.php/1237/DTITK_Sample_Data.zip | example data set]] to see what a DTI-TK compatible DTI volume looks like. Make sure the numerical values are of the same order of magnitude.
Changed line 12 from:
TVMultiply -in ${inputfile} -mult ${factor} -out ${outputfile}
to:
TVtool -in ${inputfile} -scale ${factor} -out ${outputfile}
Changed lines 24-25 from:
*'''For AFNI users''': 3dDWtoDT in AFNI does NOT factor b-value into the tensor estimation (Read more here). As a result, the program essentially always assume the b-value to be equal to 1. If the actual b-value is 1,000 s.mm'^2^', then the equivalent unit of diffusivity used by 3dDWItoDT is the same as DTI-TK. If the actual b-value is 800 s.mm'^2^', then the equivalent unit of diffusivity is 1/800 mm'^2^'.s'^-1^' instead. The multiplication factor should then be 1.25.
to:
*'''For AFNI users''': 3dDWtoDT in AFNI does NOT factor b-value into the tensor estimation (Read more [[http://afni.nimh.nih.gov/afni/community/board/read.php?f=1&i=7855&t=7855&v=f | here]]). As a result, the program essentially always assume the b-value to be equal to 1. If the actual b-value is 1,000 s.mm'^2^', then the equivalent unit of diffusivity used by 3dDWItoDT is the same as DTI-TK. If the actual b-value is 800 s.mm'^2^', then the equivalent unit of diffusivity is 1/800 mm'^2^'.s'^-1^' instead. The multiplication factor should then be 1.25.
Changed line 28 from:
*'''For FSL users''': If your b-value is 1000 s.mm'^2^' and 1000 are entered for the corresponding entries in the bvals file, then the diffusivity unit should be mm'^2^'.s'^-1^'. to:
*'''For FSL users''': If the correct b-value is used for the corresponding entries in the bval file, then the diffusivity unit should be mm'^2^'.s'^-1^'.
Changed lines 22-24 from:
Alternatively, you can compute the trace map of your DTI volumes. If you find that the trace values for CSF are close to \\
10'^-2^', then most likely it is in the unit of mm'^2^'.s'^-1^'.
to:
Alternatively, you can compute the trace map of your DTI volumes. If you find that the trace values for CSF are close to 10'^-2^', then most likely it is in the unit of mm'^2^'.s'^-1^'.
Changed lines 2-3 from:
! Important information regarding the physical diffusivity unit
to:
! Using the correct unit of diffusivity
Changed lines 11-12 from:
->[@ TVMultiply -in ${inputfile} -mult ${factor} -out ${outputfile} to:
->[@
TVMultiply -in ${inputfile} -mult ${factor} -out ${outputfile}
Changed lines 4-6 from:
to:
!!Overview
Since DTI volumes store values of physical quantities, diffusivity in this case, it is important to specify the particular physical unit used to store these values. Check this to verify that your images are stored in the right unit and to modify it if ever it is not the case.
Changed line 6 from:
The unit used by DTI-TK is 10'^-3mm^2^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3. to:
The unit used by DTI-TK is 10'^-3^'mm'^2^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3.
Changed line 6 from:
The unit used by DTI-TK is 10'^-3mm{'^2^'}^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3. to:
The unit used by DTI-TK is 10'^-3mm^2^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3.
Changed line 6 from:
The unit used by DTI-TK is 10-3mm'^2^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3. to:
The unit used by DTI-TK is 10'^-3mm{'^2^'}^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3.
Changed line 6 from:
The unit used by DTI-TK is 10'^-3mm'^2'^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3. to:
The unit used by DTI-TK is 10-3mm'^2^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3.
Changed line 6 from:
The unit used by DTI-TK is 10'^-3mm^2^^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3. to:
The unit used by DTI-TK is 10'^-3mm'^2'^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3.
Changed line 6 from:
The unit used by DTI-TK is 10'^-3mm''^2^''^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3. to:
The unit used by DTI-TK is 10'^-3mm^2^^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3.
Changed line 6 from:
The unit used by DTI-TK is 10'^-3mm'^2^'^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3. to:
The unit used by DTI-TK is 10'^-3mm''^2^''^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3.
Changed line 19 from:
Alternatively, you can compute the trace map of your DTI volumes. If you find that the trace values for CSF are close to to:
Alternatively, you can compute the trace map of your DTI volumes. If you find that the trace values for CSF are close to \\
Changed lines 20-21 from:
\\10'^-2^', then most likely it is in the unit of mm'^2^'.s'^-1^'.
to:
10'^-2^', then most likely it is in the unit of mm'^2^'.s'^-1^'.
Changed lines 20-21 from:
10'^-2^', then most likely it is in the unit of mm'^2^'.s'^-1^'.
to:
\\10'^-2^', then most likely it is in the unit of mm'^2^'.s'^-1^'.
Changed lines 19-20 from:
Alternatively, you can compute the trace map of your DTI volumes. If you find that the trace values for CSF are close to 10'^-2^', then most likely it is in the unit of mm'^2^'.s'^-1^'.
to:
Alternatively, you can compute the trace map of your DTI volumes. If you find that the trace values for CSF are close to
10'^-2^', then most likely it is in the unit of mm'^2^'.s'^-1^'.
Changed lines 19-20 from:
Alternatively, you can compute the trace map of your DTI volumes. If you find that the trace values for CSF are close to 10'^-2^', then most likely it is in the unit of mm'^2^'.s'^-1^'.
to:
Alternatively, you can compute the trace map of your DTI volumes. If you find that the trace values for CSF are close to 10'^-2^', then most likely it is in the unit of mm'^2^'.s'^-1^'.
Added lines 1-25:
(:noleft:) (:notitle:)(:title Diffusivity:)
! Important information regarding the physical diffusivity unit
!!Solving the diffusivity issue
The unit used by DTI-TK is 10'^-3mm'^2^'^'.s'^-1^'. With this unit, the mean diffusivity for CSF is around 3.
You want to make sure your DTI volumes are stored in the correct unit. If they are stored using a different unit, you can first figure out the appropriate multiplication factor, (your unit)/(DTI-TK unit), that changes the values to the unit used by DTI-TK, then use the following command to create DTI-TK compatible DTI volumes
->[@ TVMultiply -in ${inputfile} -mult ${factor} -out ${outputfile}
@]
e.g. if your DTI volumes use the unit of mm'^2^'.s'^-1^', then the multiplication factor should be 1,000. If your unit is m'^2^'.s'^-1^', then the factor should be 10'^9^'.
Here, you can download the example data set to see what a DTI-TK compatible DTI volume looks like.
!!How to figure out the unit of diffusivity in a DTI volume?
If, for diffusion-weighting, b-value of 800 s.mm'^-2^' is used during the acquisition, and you input the number 800 as the b-value to your tensor reconstruction program, then the output DTI volume will have the unit of mm'^2^'.s'^-1^'.
Alternatively, you can compute the trace map of your DTI volumes. If you find that the trace values for CSF are close to 10'^-2^', then most likely it is in the unit of mm'^2^'.s'^-1^'.
*'''For AFNI users''': 3dDWtoDT in AFNI does NOT factor b-value into the tensor estimation (Read more here). As a result, the program essentially always assume the b-value to be equal to 1. If the actual b-value is 1,000 s.mm'^2^', then the equivalent unit of diffusivity used by 3dDWItoDT is the same as DTI-TK. If the actual b-value is 800 s.mm'^2^', then the equivalent unit of diffusivity is 1/800 mm'^2^'.s'^-1^' instead. The multiplication factor should then be 1.25.
*'''For Camino users''': In general, it depends on how the scheme file is created. If the scheme file conforms to the default unit of Camino, the diffusivity unit should be m'^2^'.s'^-1^'.
*'''For FSL users''': If your b-value is 1000 s.mm'^2^' and 1000 are entered for the corresponding entries in the bvals file, then the diffusivity unit should be mm'^2^'.s'^-1^'.
|
|
