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
<ayend...@nmr.mgh.harvard.edu> wrote:
dtifit_FA.fl
t.nii.gz
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