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Size: 3373
Comment: dt_recon, diffusion tensor imaging, dti, tensormap, tracography, diffusivity, axial diffusivity, radial diffusivity, intervoxel coherence
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| USAGE: dt_recon | '''dt_recon''' |
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| Required Aruments: --i invol --b bvals bvecs --s subjectid --o outputdir |
'''Index''' <<TableOfContents>> |
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| Other Arguments (Optional) --ecref TP : Use TP as 0-based reference time points for EC --no-ec : turn off eddy/motion correction --no-reg : do not register to subject or resample to talairach --no-tal : do not resample FA to talairch space --sd subjectsdir : specify subjects dir (default env SUBJECTS_DIR) --debug : print out lots of info --version : print version of this script and exit --help : voluminous bits of wisdom |
= dt_recon = Performs processing of native diffusion tensor imaging (DTI/DWI) data. It takes original dicom images as input, and can automatically detect the bvalue and direction information from certain Siemens sequences. Other users may have to input the bvalue and direction information using bvec and bval text files with the same format as the files used in FSL diffusion processing. The subjectid refers to the subject's cortical reconstruction directory (from Freesurfer/T1 processing). This is used for registration of the diffusion data to the structural images. dt_recon outputs a variety of maps of interest in the study of neural anatomy and integrity as described in more detail below. Output maps can be entered into a variety of region of interest and voxel based analysis procedures (including TBSS from FSL). |
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| $Id: dt_recon,v 1.11 2008/07/29 19:55:17 greve Exp $ | If bvalues and bvectors are not specified with --b, it is assumed that the input is a Siemens dicom file, and gets gradient directions and bvalues based on values found in the dicom file. See $FREESURFER_HOME/diffusion/mgh-dti-seqpack/README. If the bvalues and bvectors are specified, then the input volume can be anything. The bvalues are in a simple text file, one for each direction (including b=0). The bvectors (gradient directions) are also in a simple text file with three components on each row. These also include the b=0 values. There must be as many rows in the bvals/bvecs as there are frames in the input. = Synopsis = ||dt_recon ||--i dti_dicom --s subjectid [Directive] || |
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| Performs DTI reconstruction from the raw DWI in the input file. If bvalues and bvectors are not specified with --b, it is assumed that the input is a Siemens dicom file, and gets gradient directions and bvalues from based on values found in the dicom file. See $FREESURFER_HOME/diffusion/mgh-dti-seqpack/README. If the bvalues and bvectors are specified, then the input volume can be anything. |
= Arguments = == Required Aruments == ||--i invol || input volume || ||--b bvals bvecs || b-values and b-vectors || ||--s subjectid || subject || ||--o outputdir || output directory || |
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| The bvalues are in a simple text file, one for each direction (including b=0). The bvectors (gradient directions) are also in a simple text file with three components on each row. These also include the b=0 values. There must be as many rows in the bvals/bvecs as there are frames in the input. |
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| Stages: | == Other Arguments (Optional) == ||--info-dump infodump.dat || use info dup created by unpacksdcmdir or dcmunpack || ||--ecref TP || Use TP as 0-based reference time points for EC || ||--no-ec || turn off eddy/motion correction || ||--no-reg || do not register to subject or resample to talairach || ||--no-tal || do not resample FA to talairch space || ||--sd subjectsdir || specify subjects dir (default env SUBJECTS_DIR) || ||--eres-save || save residual error (dwires and eres) || ||--pca || run PCA/SVD analysis on eres (saves in pca-eres dir) || ||--prune_thr thr || set threshold for masking (default is FLT_MIN) || ||--init-spm || init BBR with SPM instead of FSL (requires matlab) || ||--debug || print out lots of info || ||--version || print version of this script and exit || ||--help || voluminous bits of wisdom || = Stages and output = |
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| 2. Eddy current and motion correction using FSLs eddy_correct, creates dwi-ec.nii. Can take 1-2 hours. |
2. Eddy current and motion correction using FSL's eddy_correct, creates dwi-ec.nii. Can take 1-2 hours. |
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| tensor.nii -- maps of the tensor (9 frames) eigvals.nii -- maps of the eigenvalues eigvec?.nii -- maps of the eigenvectors adc.nii -- apparent diffusion coefficient fa.nii -- fractional anisotropy ra.nii -- relative anisotropy vr.nii -- volume ratio ivc.nii -- intervoxel correlation lowb.nii -- Low B bvals.dat -- bvalues bvecs.dat -- directions Also creates glm-related images: beta.nii - regression coefficients eres.nii - residual error (log of dwi intensity) rvar.nii - residual variance (log) rstd.nii - residual stddev (log) dwires.nii - residual error (dwi intensity) dwirvar.nii - residual variance (dwi intensity) 4. Registration of lowb to same-subject anatomical using FSLs flirt (creates mask.nii and register.dat) 5. Map FA to talairach space (creates fa-tal.nii) |
{{{ tensor.nii -- maps of the tensor (9 frames) eigvals.nii -- maps of the eigenvalues eigvec?.nii -- maps of the eigenvectors adc.nii -- apparent diffusion coefficient fa.nii -- fractional anisotropy ra.nii -- relative anisotropy vr.nii -- volume ratio ivc.nii -- intervoxel correlation lowb.nii -- Low B bvals.dat -- bvalues bvecs.dat -- directions }}} {{{ Also creates glm-related images: beta.nii - regression coefficients eres.nii - residual error (log of dwi intensity) rvar.nii - residual variance (log) rstd.nii - residual stddev (log) dwires.nii - residual error (dwi intensity) dwirvar.nii - residual variance (dwi intensity) }}} 4.Registration of lowb to same-subject anatomical using:bbregister (creates mask.nii and register.lta) |
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| Example usage: | 5.Map FA to talairach space (creates fa-tal.nii) |
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| dt_recon --i 6-1025.dcm --s M87102113 --o dti | = Example usage: = {{{ dt_recon --i 6-1025.dcm --s M87102113 --o dti |
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| }}} == Check registration == {{{ tkregister2 --mov dti/lowb.nii --reg dti/register.lta \ --surf orig --tag }}} == View FA on the subject's anat: == {{{ tkmedit M87102113 orig.mgz -overlay dti/fa.nii \ -overlay-reg dti/register.dat }}} Note: this only works with .dat == View FA on fsaverage == {{{ tkmedit fsaverage orig.mgz -overlay dti/fa-tal.nii }}} == Group/Higher level GLM analysis: == Concatenate FA from individuals into one file |
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| # Check registration tkregister2 --mov dti/lowb.nii --reg dti/register.dat \ --surf orig --tag # View FA on the subject's anat: tkmedit M87102113 orig.mgz -overlay dti/fa.nii \ -overlay-reg dti/register.dat # View FA on fsaverage tkmedit fsaverage orig.mgz -overlay dti/fa-tal.nii # Group/Higher level GLM analysis: # Concatenate fa from individuals into one file # Make sure the order agrees with the fsgd below |
Make sure the order agrees with the fsgd below {{{ |
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| # Create a mask: mri_concat */mask-tal.nii --o group-masksum-tal.nii --mean |
}}} == Create a mask: == {{{ mri_concat */mask-tal.nii --o group-masksum-tal.nii --mean |
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| # GLM Fit | }}} == GLM Fit == {{{ |
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| --fsgd your.fsgd --C contrast --glmdir groupanadir | --fsgd your.fsgd --C contrast --glmdir groupanadir }}} |
dt_recon
Index
Contents
dt_recon
Performs processing of native diffusion tensor imaging (DTI/DWI) data. It takes original dicom images as input, and can automatically detect the bvalue and direction information from certain Siemens sequences. Other users may have to input the bvalue and direction information using bvec and bval text files with the same format as the files used in FSL diffusion processing. The subjectid refers to the subject's cortical reconstruction directory (from Freesurfer/T1 processing). This is used for registration of the diffusion data to the structural images. dt_recon outputs a variety of maps of interest in the study of neural anatomy and integrity as described in more detail below. Output maps can be entered into a variety of region of interest and voxel based analysis procedures (including TBSS from FSL).
If bvalues and bvectors are not specified with --b, it is assumed that the input is a Siemens dicom file, and gets gradient directions and bvalues based on values found in the dicom file. See $FREESURFER_HOME/diffusion/mgh-dti-seqpack/README. If the bvalues and bvectors are specified, then the input volume can be anything.
The bvalues are in a simple text file, one for each direction (including b=0). The bvectors (gradient directions) are also in a simple text file with three components on each row. These also include the b=0 values. There must be as many rows in the bvals/bvecs as there are frames in the input.
Synopsis
dt_recon |
--i dti_dicom --s subjectid [Directive] |
Arguments
Required Aruments
--i invol |
input volume |
--b bvals bvecs |
b-values and b-vectors |
--s subjectid |
subject |
--o outputdir |
output directory |
Other Arguments (Optional)
--info-dump infodump.dat |
use info dup created by unpacksdcmdir or dcmunpack |
--ecref TP |
Use TP as 0-based reference time points for EC |
--no-ec |
turn off eddy/motion correction |
--no-reg |
do not register to subject or resample to talairach |
--no-tal |
do not resample FA to talairch space |
--sd subjectsdir |
specify subjects dir (default env SUBJECTS_DIR) |
--eres-save |
save residual error (dwires and eres) |
--pca |
run PCA/SVD analysis on eres (saves in pca-eres dir) |
--prune_thr thr |
set threshold for masking (default is FLT_MIN) |
--init-spm |
init BBR with SPM instead of FSL (requires matlab) |
--debug |
print out lots of info |
--version |
print version of this script and exit |
--help |
voluminous bits of wisdom |
Stages and output
1. Convert input to nifti (creates dwi.nii)
2. Eddy current and motion correction using FSL's eddy_correct, creates dwi-ec.nii. Can take 1-2 hours.
3. DTI GLM Fit and tensor construction. Includes creation of:
tensor.nii -- maps of the tensor (9 frames) eigvals.nii -- maps of the eigenvalues eigvec?.nii -- maps of the eigenvectors adc.nii -- apparent diffusion coefficient fa.nii -- fractional anisotropy ra.nii -- relative anisotropy vr.nii -- volume ratio ivc.nii -- intervoxel correlation lowb.nii -- Low B bvals.dat -- bvalues bvecs.dat -- directions
Also creates glm-related images: beta.nii - regression coefficients eres.nii - residual error (log of dwi intensity) rvar.nii - residual variance (log) rstd.nii - residual stddev (log) dwires.nii - residual error (dwi intensity) dwirvar.nii - residual variance (dwi intensity)
4.Registration of lowb to same-subject anatomical using:bbregister (creates mask.nii and register.lta)
5.Map FA to talairach space (creates fa-tal.nii)
Example usage:
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals f.bvecs --s M87102113 --o dti
Check registration
tkregister2 --mov dti/lowb.nii --reg dti/register.lta \ --surf orig --tag
View FA on the subject's anat:
tkmedit M87102113 orig.mgz -overlay dti/fa.nii \ -overlay-reg dti/register.dat
Note: this only works with .dat
View FA on fsaverage
tkmedit fsaverage orig.mgz -overlay dti/fa-tal.nii
Group/Higher level GLM analysis:
Concatenate FA from individuals into one file
Make sure the order agrees with the fsgd below
mri_concat */fa-tal.nii --o group-fa-tal.nii
Create a mask:
mri_concat */mask-tal.nii --o group-masksum-tal.nii --mean mri_binarize --i group-masksum-tal.nii --min .999 --o group-mask-tal.nii
GLM Fit
mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\ --fsgd your.fsgd --C contrast --glmdir groupanadir