Dear Colleagues,

I have been trying to run the preprocessing script on my resting state data (v. 1.1b), and I keep running into errors during the nuisance signal regression stage. What I keep getting is below:

Modifying model file
Running feat model
Not enough data in /Users/Duke/scripts/test/01626306/func/nuisance/csf.1D
Running film to get residuals
Log directory is: /Users/Duke/scripts/test/01626306/func/nuisance/stats


An exception has been thrown
Unable to open /Users/Duke/scripts/test/01626306/func/nuisance/nuisance.mat
++ 3dTstat: AFNI version=AFNI_2009_12_31_1431 (Jul 23 2010) [64-bit]
++ Authored by: KR Hammett & RW Cox
** FATAL ERROR: Can't open dataset /Users/Duke/scripts/test/01626306/func/nuisance/stats/res4d.nii.gz
** Program compile date = Jul 23 2010
++ 3dcalc: AFNI version=AFNI_2009_12_31_1431 (Jul 23 2010) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset /Users/Duke/scripts/test/01626306/func/nuisance/stats/res4d.nii.gz
** Program compile date = Jul 23 2010
** ERROR (nifti_image_read): failed to find header file for '/Users/Duke/scripts/test/01626306/func/4DI001_res'
** ERROR: nifti_image_open(/Users/Duke/scripts/test/01626306/func/4DI001_res): bad header info
Error: failed to open file /Users/Duke/scripts/test/01626306/func/4DI001_res
ERROR: Could not open image /Users/Duke/scripts/test/01626306/func/4DI001_res
Image Exception : #22 :: Failed to read volume /Users/Duke/scripts/test/01626306/func/4DI001_res
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/Users/Duke/scripts/5_nuisance.sh: line 95: 63891 Abort trap flirt -ref ${reg_dir}/standard -in ${func_dir}/${rest}_res -out ${func_dir}/${rest}_res2standard -applyxfm -init ${reg_dir}/example_func2standard.mat -interp trilinear

I'm guessing it has something to do with nuisance.mat, and I don't seem to get that file after I run the script. If you have any ideas as to why I keep getting this error, and particularly any ways that I could fix this, I would be greatly appreciative.

Many thanks in advance and all the best.

Duke