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Hi Joe, looks like something quite low-level failed as it bails out right at the beginning… maybe you don’t have write permission where you’re trying to run things? One initial thing to make sure is that all run data is proper 4d nifti, e.g by loading it into fslview and checking that fslsize gives what you’d expect in terms of number of volumes etc. Also, if there are NaNs in your data your may want to pass it through fslmaths first. Also, make sure that file and directory permissions are OK and that FSLDIR is set to /usr/local in your case. hth Christian > On 16 Dec 2014, at 05:25, Jonathan Starke <[log in to unmask]> wrote: > > Hi FSL team, > > have a functional data set of 15 patients and 10 controls subjects. patients scanned on 2 ocassions each so 30 scans, and controls scanned once only so 10 scans. total of 40 4D nifti files as input. will be running resting state analysis using the 10 Smith 2009 components available on FSL. therefore do NOT need to run ICA to identify components, BUT do need to do pre-processing of data (motion correction, BET etc) and registration so that i can then do dual regression of my data using Smith components. have been advised to do pre-precessing in melodic. therefore, set up basic MELODIC plan using GUI and ran it, but get following (in report_log): > > /bin/cp /tmp/feat_6OgThP.fsf design.fsf > > mkdir .files;cp /usr/local/fsl/doc/fsl.css .files;ln -s /usr/local/fsl/doc/images .files/images > > FATAL ERROR ENCOUNTERED > > not sure what to make of it. 2 things occurred to me that i may have done wrong: > 1) my input data are 4D nifti files, but i have done nothing else to them - should i have done some other processing (possibly in FEAT?) prior to using them in melodic? > 2) i dont have subject-specific structural scans, so am registering directly from functional to MNI space. i understand that while not ideal, this should not be a technical problem, BUT do the voxel dimensions of my func scans and the MNI template need to be the same? (at mo my func data is 3.4 by 3.4 by 3mm and i am using a 2mm MNI brain as per standard GUI setting). if yes, how do i trasnform func data into right dimensions? applywarp? applyxfm? - have not done this before. > > am happy to send example of input data and design.fsf if this is needed. > > thanks for the help > joe starke > masters student > university of cape town