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

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

-  ⇤ ← Revision 1 as of 2008-12-30 10:55:07 → 
  Size: 3373
  Editor: DavidSalat
  Comment: dt_recon, diffusion tensor imaging, dti, tensormap, tracography, diffusivity, axial diffusivity, radial diffusivity, intervoxel coherence
+   ← Revision 19 as of 2018-02-05 10:22:25 → ⇥
  Size: 4630
  Editor: MorganFogarty
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-USAGE: dt_recon
+'''dt_recon'''
 Line 3:
- Required Aruments:
   --i invol
   --b bvals bvecs
   --s subjectid
   --o outputdir
+'''Index''' <<TableOfContents>>
-Line 9:
+Line 5:
- 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).
-Line 19:
+Line 8:
-$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] ||
-Line 22:
+Line 16:
-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 ||
-Line 29:
+Line 23:
-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.
-Line 35:
+Line 24:
-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 =
-Line 37:
+Line 42:
-. Eddy current and motion correction using FSLs eddy_correct,
   creates dwi-ec.nii. Can take 1-2 hours.
+. Eddy current and motion correction using FSL's eddy_correct, creates dwi-ec.nii. Can take 1-2 hours.
-Line 40:
+Line 46:
-   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)
-Line 62:
+Line 70:
-Example usage:
+.Map FA to talairach space (creates fa-tal.nii)
-Line 64:
+Line 72:
-dt_recon --i 6-1025.dcm --s M87102113 --o dti
+= Example usage: =
{{{
dt_recon --i 6-1025.dcm --s M87102113 --o dti
-Line 66:
+Line 77:
+}}}
== Check registration ==
tkregister2 --mov dti/lowb.nii --reg dti/register.lta \
-Line 67:
+Line 81:
-# Check registration
tkregister2 --mov dti/lowb.nii --reg dti/register.dat \
  --surf orig --tag
+ . --surf orig --tag
-Line 71:
+Line 83:
-# View FA on the subject's anat:
+== View FA on the subject's anat: ==
-Line 73:
+Line 85:
-   -overlay-reg dti/register.dat
-Line 75:
+Line 86:
-# View FA on fsaverage
+ . -overlay-reg dti/register.dat

== View FA on fsaverage ==
-Line 78:
+Line 91:
-# Group/Higher level GLM analysis:
# Concatenate fa from individuals into one file
#  Make sure the order agrees with the fsgd below
+== Group/Higher level GLM analysis: ==
== Concatenate FA from individuals into one file ==
== Make sure the order agrees with the fsgd below ==
-Line 82:
+Line 95:
-# 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
+== 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 ==
-Line 87:
+Line 101:
-    --fsgd your.fsgd --C contrast --glmdir groupanadir
+ . --fsgd your.fsgd --C contrast --glmdir groupanadir