This is a bug that popped up because the Linux developers changed a shell script behavior in the most recent CentOS. You can get a fix from here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister

doug

On 04/02/2013 04:18 PM, Mario Ortega wrote:

Hi freesurfer team, I have been having intermittent problems ( Im assuming bbregister problems.) the register.dof6.dat file is not being written, and I find an error in the dat.log

error is here: flirt.fsl -ref bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister.nii -in bold/011/tmp.bbregister.10308/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/011/tmp.bbregister.10308/fslregister/fslma t0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init bold/011/tmp.bbregister.10308/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for 'bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister): bad header info Error: failed to open file bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister ERROR: Could not open image bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped)

I do have disk space. the command that I use is preproc-sess -s FCBA05_MR1 -fsd bold -per-run -stc siemens -force -surface fsaverage rhlh -fwhm 6

Any help is appreciated as I continue tracing the error. Thanks, Mario

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