Hi Natalia - This is an error that will occur if lowb_brain_mask does not exist. The command that generates lowb_brain_mask is "bet" - can you find that line in the log file and run it directly on the command line and see if you get an error?

On a separate note, have you opted to use a DWI mask instead of an anatomical mask by setting usemaskanat = 0? If not, then it may be that it's trying to use the DWI mask b/c it can't find the anatomicals, in which case I'd check if SUBJECTS_DIR has been set properly and a freesurfer recon of the same subject exists there. But this is a separate issue than the DWI mask not being generated.

Hope this helps, a.y

On Fri, 10 Aug 2012, Natalia Sánchez wrote:

The required files were not generated.

the error occurs at

rh.slft_PP_roi2.flt.nii.gz --bmask/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain _mask.flt.nii.gz --fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.fl t.nii.gz --ncpts 5 --trunc --debug ERROR: fio_pushd: /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni ERROR: Must specify brain mask volume for output subject

does the brain mask have to be input manually in the configuration file, or is this part of the pre-processing? since I set the bet thr to 0.23 in the config file i thought the brain mask was also created during the preprocessing stage. Attached is my log file.

I am familiar with FSL but I am using Free surfer since i think automating the entire process, including tracking is a great advantage, but I'm just starting to get the hang of it

Thanks!

-- Natalia Sánchez     PhD Candidate     Departments of Biomedical Engineering &     Physical Therapy and Human Movement Sciences    Northwestern University     645 North Michigan Ave, Suite 1100     Chicago, IL 60611

On Fri, Aug 10, 2012 at 4:28 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote: dtifit_FA.fl t.nii.gz