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?
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.