afni.nimh.nih.gov

Thanks pt, here are the processing steps involved for the files you asked about:

1) 3dDWItoDT_*

3dDWItoDT \
-prefix 3dDWItoDT.nii.gz \
-automask \
-reweight \
-max_iter 10 \
-max_iter_rw 10 \
-eigs \
-sep_dsets \
-bmatrix_FULL dwi_matA.txt \
dwi_ec_allin.nii.gz \
-scale_out_1000 \
-overwrite


2) DWUncert+orig

3dDWUncert \
-inset dwi_ec_allin.nii.gz \
-prefix DWUncert \
-input 3dDWItoDT_ \
-bmatrix_FULL dwi_matA.txt \
-iters 50 \
-overwrite

3) $dtipath/{}/MASK.nii.gz
To be honest I can't remember *exactly* what I did but it is a binary mask. I have attached a screenshot of what it looks like. (is masking even recommended?)

4) $dtipath/{}/mri/parc5002dwi.nii.gz
Making this netrois file required a number of steps in Freesurfer. The original parcellation (two separate .annot files, one for each hemisphere) is based off the fsaverage_sym template.
-I ran mri_surf2surf to resample from fsaverage_sym onto each subject.
-I then combined lh .annot and rh .annot into a bilateral .nii.gz using mri_aparc2aseg.
-As the parcellation should only be cortical, but mri_aparc2aseg automatically labels subcortical as well, I ran a matlab script to remove the subcortical labels.
-I ran bbregister to get the transformation matrix from dti into T1 space.
-I then used the inverse transformation matrix to get the parcellation (which is in T1 space) to dti space.
-I confirm that this final netrois file is now in dti space and contains 318 parcels.
I hope this wasn't too confusing.


Also, you asked what the output of 3d info is. Not sure what this output indicates but hope it's informative:
NO-DSET NO-DSET NO-DSET
0.000 0 parc5002dwi.nii.gz
0.000 0 MASK.nii.gz
NO-DSET NO-DSET NO-DSET

Thanks for your feedback on what might have gone awry.