Hello. Lengthy post warning!
I’m trying to create a pipeline for my DTI-data through the use of the B.A.T.M.A.N- tutorial. I’ve come across some challenges, though. I’m sorry for the many different questions.
My raw DTI-series is acquired PA, along with two separate reference b0-acquisitions;AP and PA, respectively. B-values: 0 and 1000.
I’ve done the following:
mrconvert DTI.nii.gz -fslgrad bvecs bvals DTI.mif
dwidenoise DTI.mif DTI_den.mif -noise noise.mif
mrcalc DTI.mif DTI_den.mif -subtract residual.mif
#The residual map clearly depicted the large ventricles; what does that imply? And for the noise; how do you evaluate that?
mrcalc DTI_den.mif DTI_den_unr.mif -subtract residualUnringed.mif
#how to evaluate this?
dwiextract DTI_den_unr.mif - -bzero | mrmath - mean mean_b0_PA.mif -axis 3
mrconvert AP.nii.gz AP.mif
mrcat mean_b0_PA.mif AP.mif -axis 3 b0_pair.mif
dwifslpreproc DTI_den_unr.mif DTI_den_unr_preproc.mif -pe_dir PA -rpe_pair -se_epi b0_pair.mif -nocleanup
#should I run -eddy_options " --slm=linear" here? Or “-eddyqc_*”?
#I didn’t run dwibiascorrect… pros and cons for this?
dwi2mask DTI_den_unr_preproc.mif mask_den_unr_preproc.mif
mrview mask_den_unr_preproc.mif -colourmap 2
dwi2response dhollander DTI_den_unr_preproc.mif wm.txt gm.txt csf.txt -voxels voxels.mif
mrview DTI_den_unr_preproc.mif -overlay.load voxels.mif
#I understood from a previous post of mine that the gm-file should be ignored in the subsequent analysis. Should I have run this command without it? The dots representing WM and CSF- voxels appeared similar as in the tutorial, whilst the GM-voxels appeared in slightly different locations than in the tutorial, yet still in what appeared to be GM.
shview wm.txt
shview gm.txt
shview csf.txt
#These looked similar to the response functions in the tutorial
dwi2fod msmt_csd DTI_den_unr_preproc.mif -mask mask_den_unr_preproc.mif wm.txt wmfod.mif csf.txt csffod.mif
mrconvert –coord 3 0 wmfod.mif -| mrcat csffod.mif –vf.mif
#I couldn’t get the quality control of the FOD-etimation to work (Figure 7, p.13-14).I removed gmfod.mif from the command since I don’t have it, I suppose that is why I can’t seem to get the quality control up-and- running, or? I got multiple errors.
It is unfortunate not to be able to achieve GM-status, I am really insecure about how to proceed.
mtnormalise wmfod.mif wmfod_norm.mif csffod.mif csffod_norm.mif -mask mask_den_unr_preproc.mif
#I removed gmfod.mif gmfod_norm.mif from the command.
mrconvert T1.nii T1.mif
5ttgen fsl T1.mif 5tt_nocoreg.mif
#A black hole appears above the right ventricle; as if some mistake has occurred during segmentation. What have I done wrong/could I have done differently? It should be noted that the ventricles in this case are slightly enlarged. Could that be of influence?
dwiextract DTI_den_unr_preproc.mif - -bzero | mrmath - mean mean_b0_preprocessed.mif -axis 3
mrconvert mean_b0_preprocessed.mif mean_b0_preprocessed.nii.gz
mrconvert T1.mif T1.nii.gz
flirt -in mean_b0_preprocessed.nii.gz -ref T1.nii.gz -dof 6 -omat diff2struct_fsl.mat
transformconvert diff2struct_fsl.mat mean_b0_preprocessed.nii.gz T1.mif flirt_import diff2struct_mrtrix.txt
mrtransform T1.mif -linear diff2struct_mrtrix.txt -inverse T1_coreg.mif
mrtransform 5tt_nocoreg.mif -linear diff2struct_mrtrix.txt -inverse 5tt_coreg.mif
mrview DTI_den_unr_preproc.mif –overlay.load T1.mif –overlay.colourmap 2 -overlay.load T1_coreg.mif –overlay.colourmap 1
#I get the following error when I try to run the last command for mrview: “Error. Options must appear after the last argument”. When manually opening the three images, it looks as if the T1coreg has been somewhat angled compared to T1.mif and DTI_den_unr_preproc.mif. It looks as if the T1 and DTI are acceptably aligned, with the T1coreg being lowered. If that makes sense.
5tt2gmwmi 5tt_coreg.mif gmwmSeed_coreg.mif
mrview DTI_den_unr_preproc.mif -overlay.load gmwmSeed_coreg.mif
#As mentioned and as a result of the above; the gmwmSeed_coreg overlaid on the DTI appears lower and not “in the right place”. In addition some skull is included in the seed.
Well, a long one. Thank you so much for any input and your time!