Hi Paul,

How to adapt your FATCAT tutorial for HARDI modelling?

I did some try, but not worked very well.

My adaptation start at the "Post-preproc, I: tensor estimation and checking" step.
As the number of my PA volumes is not equal to that of AP, the "ap_proc_DRBUDDI_up_final.nii" is the final output from DR_BUDDI.

# HARDI estimates with DSI studio, with flip chosen from @GradFlipTest
    
# Get a column of b-value information for DTI-Studio
1dDW_Grad_o_Mat++                                                                           \
        -in_col_matT    $itort/ap_proc_DRBUDDI_up_final.bmtxt       \
        -unit_mag_out                                                                                 \
        -flip_z         $my_flip                                                                        \
        -out_col_bval                                                                                   \
        -out_col_vec    $itort/ap_proc_DRBUDDI_up_final_b_table.txt

After that, I run "do_dsistudio.tcsh" script at FATCAT_DEMO/HARDI with ap_proc_DRBUDDI_up_final.nii.gz+b_table.txt, and got GQI_gfa.nii.gz.

However, the orient of the GFA is different from other dataset mapped to dwi_dwi. This problem can be seen in FATCAT_DEMO/GQI_GFA.nii.gz too:

GQI_GFA.nii.gz
R-to-L extent:  -254.000 [R] -to-    -0.000     -step-     2.000 mm [128 voxels]
ROI_ICMAP_GMI+orig
R-to-L extent:  -129.041 [R] -to-   124.959 [L] -step-     2.000 mm [128 voxels]

Does this affects the tracking results? (But this do affects viewing.)
I tried 3dresample the GQI_GFA to dwi, but the volume still located at the corner.
Or should I map all other dataset to GQI_GFA space?

I tired to ignore this problem, and run 3dTrackID with the uncertainty calced like "Do_07_RUNhardi_uncertainty_est.tcsh" (And is there any new uncertainty estimator?):

3dTrackID                                               	            \
        -mode               PROB                            	    \
        -hardi_gfa          GQI_gfa.nii.gz                          \
        -hardi_dirs         GQI_dirs.nii.gz                         \
        -netrois            fmri_msk_${subj}_GMI.nii.gz    \
        -uncert             Simple_Uncert.nii.gz                  \
        -unc_min_FA         0.0015                                  \
        -dump_rois          AFNI                                       \
        -alg_Thresh_FA      0.04                             	    \
        -alg_Thresh_Frac    0.011                             	    \
        -alg_Nseed_Vox      5                               	    \
        -alg_Nmonte         1000                            	    \
        -prefix             fPROB_${subj}              	            \
        -nifti -write_opts -overwrite -echo_edu

As the picture see, all negative.



Thank you
2086



Edited 3 time(s). Last edit at 05/30/2018 09:02AM by EXP.2086.