I'm trying to transform a mean functional image into subject (T1) space using mri_vol2vol.  Originally, my code worked successfully, but in attempts to re-run the procedure, both on the same data and on additional data, I've encountered an error in which the log reports an "ERROR: Option unknown" and also "--o: command not found."  

I am hoping to resolve this issue; does anyone see where my issue is arising from?  This is especially strange given that I've gotten it to work before, and I don't think I made any changes to the script besides changing the directory locations for different subjects' data.  

Here is the mri_vol2vol command as I currently have it:

mri_vol2vol --reg ${iSub}_bbregister.dat --mov ${iSub}_Tempfiltered_mean.nii --targ ${DataDir}/S1/${iSub}/${iSub}_brainmask.gcuts.nii \ 

--o ${iSub}_mean_epi_inT1.nii

The cd is ${DataDir}/S1/${iSub} , which contains the ${iSub}_bbregister.dat , ${iSub}_Tempfiltered_mean.nii , and ${iSub}_brainmask.gcuts.nii files.  

Thanks for your help,

Ben Mooneyham

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Graduate Student
UCSB - Department of Psychological & Brain Sciences
Building 429 Room 102
(210) 912-6076
bwmooneyham@gmail.com