Hi,

I have some mouse resting state fMRI data that I have already co-registered using the FSL package. I would like to use the CONN toolbox (17.c, run with MatlabR2014a) to perform seed-to-voxel and voxel-to-voxel analyses. I have entered data from 3 different subjects with their co-registered anatomicals, and 1 rsfmri file each. For pre-processing, I have selected the following steps (I do not want any normalization to MNI atlas or centering to coordinates).

functional Realignment (subject motion estimation and correction)
functional Slice-timing correction
functional Outlier detection (ART-based identification of outlier scans for scrubbing)
functional Smoothing (spatial convolution with Gaussian kernel)

Everything ran successfully, so I proceeded to the next step. CONN started normalization, and then quickly after the following error message appeared.

ERROR DESCRIPTION:

Error using conn_setup_preproc (line 185)
STEP name %s is not a valid preprocessing step or an existing preprocessing-pipeline file
Error in conn_process (line 240)
conn_setup_preproc('run_structural_segment','subjects',nsub);
Error in conn_process (line 15)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 4119)
else conn_process('setup'); ispending=false;
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.17.c
SPM8 + Beamforming DEM FieldMap MEEGtools
Matlab v.2014a
storage: 39.2Gb available
spm installed in folder /Users/kchoe/Documents/MATLAB/spm8
Warning: Contents.m overloaded by version in folder /Users/kchoe/Documents/MATLAB/uf2c_7_0
conn installed in folder /Users/kchoe/Documents/MATLAB/conn

Could you please help me fix this issue? I think it has something to do with my preprocessing pipeline, since when I select the "default preprocessing pipeline for volume-based analysis (direct normalization to MNI-space)" the whole thing runs without error, although I don't get any useful data out of it.

Thanks so much in advance for your help.

Katrina