Welcome to my scripts to Dicom images

heudiconv.py

This scripts is a GUI to heudiconv. You need to copy the paths to original images, destinatios folder and your heuristic file. In the GUI you need to introduce the codes to convert into BIDS. Is just a silly tool with GUI to create a easy way to convert images based on Heudiconv.

slicecal.py

Sometimes when you manage dicom images from Philips scanner the conversion to nifit with dcm23niix the slicetiming is missing. With this calculator you could have the section of slice timing to insert in yor json. You need to know TR, Slices and Order.

Pipeline to work with CAMINO to estimate DTI

Install CAMINO, FSL and ANTs

files and path:
--|Code
----|DWI
------|data.nii.gz ------|bvecs ------|bvals ----|T1
------|T1.nii.gz

for code in $(cat ~/codelist.txt) do

cd $path/$code/

mkdir CAMINO
mkdir DTIFIT
mkdir DTItk
cp -R DTI DWI

cd $path/$code/DWI

correction with FSL

fsl5.0-eddy_correct $DWI data.nii.gz 1
cp xDTIhighisoSENSE_33.bvec bvecs
cp bvecs bvectemp
mv bvecs bvectemp

convert bvals and bvecs to Camino format

psc -r < bvectemp | sc -W% - > grad_dirs.txt
rm bvectemp	

BET extraction

fsl5.0-bet $DWI nodif_brain.nii.gz -f .3 -m

cp nodif_brain_mask.nii.gz $path/$code/CAMINO
cp grad_dirs.txt $path/$code/CAMINO

Model Estimation with Camino

cd $path/$code/CAMINO

pointset2scheme -inputfile grad_dirs.txt -bvalue 1E9 -outputfile 4Ddwi_b_bvector.scheme
image2voxel -4dimage ../DWI/data.nii.gz -outputfile dwi.Bfloat

dtfit dwi.Bfloat 4Ddwi_b_bvector.scheme -bgmask nodif_brain_mask.nii.gz -outputfile dt.Bdouble
modelfit -inversion 2 -schemefile 4Ddwi_b_bvector.scheme -inputfile dwi.Bfloat -bgmask nodif_brain_mask.nii.gz > dt_nonlinear.Bdouble


	for PROG in fa md; do
	  cat dt.Bdouble | ${PROG} | voxel2image -outputroot ${PROG} -header ../DWI/$DWI
	done
cat dt_nonlinear.Bdouble | dteig > dteig.Bdouble
dt2nii -inputfile dt_nonlinear.Bdouble -outputroot nifti_ -header ../DWI/$DWI
#visualizador de primer nivel de Camino
#pdview -inputfile dteig.Bdouble -scalarfile fa.nii.gz

cd $path/$code/
fsl5.0-dtifit -k DWI/data.nii.gz -o DTIFIT/data -m DWI/nodif_brain_mask.nii.gz -r DWI/bvecs -b DWI/bvals -w

done