Errors with AFQ pipeline

[nasiametoki]

Hello,

I am encountering some issues when running AFQ_run.

I preprocessed my data with FSL so I created the 'dt6.mat' file using the dtiMakeDt6FromFsl function. Then I tried running AFQ_run.

I have created this script to run AFQ_run for one subject:

sub_dirs = '/Users/Imaging/345/Pre_processed_DTI';
afq = AFQ_Create('run_mode', 'sub_dirs', sub_dirs);
[afq abn abnTracts] = AFQ_run(sub_dirs, afq)

Here are the results and the errors of this script:

Performing whole-brain tractograpy for subject /Users/Imaging/345/Pre_processed_DTI

scale=[2.0,2.0,2.5]mm, track=1, interp=1, step=1.0mm, fa=0.20, angle=30.0deg, puncture=0.20, minLength=50.0mm, maxLength=250.0mm
Tracking 236672 fibers (2959 fibers per tick):
................................................................................
126251 fibers passed length threshold of 50.0 (out of 236672 seeds).
Elapsed time is 286.924041 seconds.
126251 fibers, mean length 94mm (max 251mm; min 50mm).
You chose to recompute ROIs
Fibers that get as close to the ROIs as 2mm will become candidates for the Mori Groups
Smoothing by 0 & 8mm..
Coarse Affine Registration..
Fine Affine Registration..
3D CT Norm...
iteration 1: FWHM = 16.66 Var = 116.251
iteration 2: FWHM = 8.607 Var = 0.923147
iteration 3: FWHM = 7.935 Var = 0.613146
iteration 4: FWHM = 7.993 Var = 0.584254
iteration 5: FWHM = 7.883 Var = 0.572802
iteration 6: FWHM = 7.912 Var = 0.569482
iteration 7: FWHM = 7.875 Var = 0.56696
iteration 8: FWHM = 7.886 Var = 0.566065
iteration 9: FWHM = 7.873 Var = 0.565546
iteration 10: FWHM = 7.881 Var = 0.565546
iteration 11: FWHM = 7.875 Var = 0.565161
iteration 12: FWHM = 7.876 Var = 0.565057
iteration 13: FWHM = 7.875 Var = 0.565057
iteration 14: FWHM = 7.876 Var = 0.564906
iteration 15: FWHM = 7.877 Var = 0.564906
iteration 16: FWHM = 7.876 Var = 0.564806
Computing inverse deformation...
dtiCleanFibers: Keeping 126079 out of 126251 fibers.
dtiSplitInterhemisphericFibers: Splitting every fiber below Z=-10

Computing Tract Profiles for subject //Users/Imaging/345/Pre_processed_DTIUndefined operator '==' for input arguments of type 'struct'.

Error in AFQ_set (line 163)
afq.norms.(['mean' upper(valnames{ii})])(:,jj) =
nanmean(afq.vals.(valnames{ii}){jj}(afq.sub_group==0,:));

Error in AFQ_ComputeNorms (line 37)
afq = AFQ_set(afq,'norms');

Error in AFQ_run (line 326)
[norms, patient_data, control_data, afq] = AFQ_ComputeNorms(afq);

Error in afq_test (line 4)
[afq abn abnTracts] = AFQ_run(sub_dirs, afq)

The outputs I get despite these errors are these:
fibers->MoriGroups_clean_D5_L4.mat, MoriGroups.mat, WholeBrainFG.mat
ROIs->ATR_roi1_L.mat, ATR_roi1_R.mat, ATR_roi2_L.mat, ATR_roi2_R.mat, CGC_roi1_L.mat, CGC_roi1_R.mat ... etc

Questions:
a) Is there anything wrong in the syntax of my script?
b) What are these errors I am getting and how can they be fixed?
c) What is each file in the "fibers" folder?
d) According to this example: http://yeatmanlab.github.io/AFQ/tutorials/AFQ_example#3, steps 3, 4, and 5 did not run for me. Is this correct? Also, I am not getting this message "mesh can be rotated with arrow keys", does this mean that something is not right?

Thank you!

Best,
Nasia M.