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anoushkrit / parcellation

preprocessing pipeline for handling raw neuroimaging data and conducting various file conversions
https://supwma.github.io
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create .trk from .nii.gz , .bval and .bvec #5

Closed anoushkrit closed 2 years ago

anoushkrit commented 2 years ago

usually the raw data has .nii.gz, .bval, .bvec but we need .trk from these 3 inputs to work futher

anoushkrit commented 2 years ago

something to look for https://community.mrtrix.org/t/dwi2tensor-on-roi-image-in-tck-file-format/4149

anoushkrit commented 2 years ago

mrtrix commands connectome2tck: converting dwi .niigz to tracts .tck tckmap: converting .tck (tracts file) to .mif file dwi2tensor: converting the .mif (tracts) file to dt \

anoushkrit commented 2 years ago

https://www.nitrc.org/plugins/mwiki/index.php?title=ukftractography:Options

anoushkrit commented 2 years ago 
mrconvert data.nii.gz DWI.mif -fslgrad bvecs bvals -datatype float32 -strides 0,0,0,1
5ttgen fsl T1w_acpc_dc_restore_1.25.nii.gz 5TT.mif
dwi2response msmt_5tt DWI.mif 5TT.mif rf_wm.txt rf_gm.txt rf_csf.txt -voxels rf_voxels.mif
dwi2fod msmt_csd DWI.mif rf_wm.txt wm_fods.mif rf_gm.txt gm.mif rf_csf.txt csf.mif -mask nodif_brain_mask.nii.gz
tckgen -algorithm iFOD2 wm_fods.mif output.tck -act 5TT.mif -backtrack -crop_at_gmwmi -seed_image nodif_brain_mask.nii.gz -maxlength 250 -minlength 40 -select 10M -cutoff 0.06