Unwarping of B0 inhomogeneity distortion, correction of eddy current distortion and motion, tensor calculation and QC
Before installation of dti_preprocess, you need to install FSL (>5.0). You also require gdcmdump and HCP pipleine for scripts, getdwelltime and regdtiprep2hcp, respectively.
- After uncompressing the downloaded dti_preprocess.zip, move dti_preprocess into /usr/local
sudo mv dti_preprocess /usr/local/
- Add the following lines in .bashrc in your home directory
export DTI_PREPROCESS=/usr/local/dti_preprocess;
export PATH=${DTI_PREPROCESS}/bin:${PATH};
-
Modify the section of "Default environments" in
/usr/local/dti_preprocess/etc/conf/dti_preprocess.conf, depending on your environments. -
Open new terminal and run dti_preprocess so that you should be able to see the help page
dti_preprocess
Usage 1: Minimal data-based correction (using eddy_correct)
dti_preprocess -k <dwi> -b <bvals> -r <bvecs> [option]
-k <dwi> : dwi 4D data
-b <bvals> : a text file containing a list of b-values
-r <bvecs> : a text file containing a list of b-vectors
Usage 2: Data-based correction (using fieldmap, fugue and eddy_correct)
2.1 Run fieldmap correction only :
dti_preprocess -k <dwi> -t <num> -f <img> -m <img> [option]
2.2 Run both fieldmap and eddy-current correction :
dti_preprocess -k <dwi> -b <bvals> -r <bvecs> -t <num> -f <img> -m <img> [option]
-t <num> : dwell time (ms) of dwi in phase-encoding direction (divided by accerelation factor)
-f <img> : B0 fieldmap image (radian/sec)
-m <img> : B0 fieldmap magnitude image
Options:
-u <x, x-, y, y-, z, or z-> : unwarp direction (default: y-)
-D <img> : mask file for dti image (by default, this is calculated by bet)
-M <img> : mask file for fieldmap magnitude image (by default, this is calculated by bet)
-E <num> : reference volume (default : 0th volume)
-n : do not register between fieldmap and dti data (requires to register beforehand)
-U : do not mask DTI images
Usage 3: Model-based correction (using blip-up and down data, topup and eddy)
3.1 Run fieldmap correction only :
dti_preprocess -k <dwi> -K <dwi-PER> -t <num> [options]
3.2 Run both fieldmap and eddy-current correction :
dti_preprocess -k <dwi> -b <bvals> -r <bvecs> -K <dwi-PER> -B <bvals-PER> -R <bvecs-PER> -t <num> [options]
-K <dwi-PER> : dwi 4D data with phase-encode reversed (PER)
-B <bvals-PER> : bvals for dwi-PER
-R <bvecs-PER> : bvecs for dwi-PER
-t <num> : dwll time (ms) of dwi in phase-encoding direction
Options:
-u <x or y> : phase-reversed direction (default: y)
-p : optimized for single-shell data
-w : potentially better converge if there is substantial subject movement
General options applied for all usages:
-o <dir> : output directory (default is <dwi 4D data>.prep)
-F : use the actual directory name given (i.e. do not add + to make a new directory)
-c : use mcflirt instead of flirt (faster but may not be accurate)
-H <HCP subject dir> : registeter to HCP pipelined directory and run QA
-v : verbose
-h : output help page