Hi Freesurfer experts,

I was running recon-all on a cluster and encountered the following error:

mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

Linux compute-g20-12.deepthought.umd.edu 2.6.18-371.3.1.el5 #1 SMP Mon Nov 11 03:23:58 EST 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s hcp80100307 exited with ERRORS at Wed May 21 12:43:36 EDT 2014

Any idea whats the source of the error?

Thanks!

On Wed, May 21, 2014 at 2:20 PM, C.P. Frost cpfrost@wisc.edu wrote:

Hello all,

My site has recently upgraded to the newest version of Freesurfer, and I've run a set of subjects on recon-all using the hippocampal subfield segmentation flag. Everything went well. Then in running kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages indicating that certain expected files didn't exist.

In particular, among output files labeled with the scheme $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz -- in other words, the script expected a hyphen but instead the filenames contained an underscroe.

After renaming the files appropriately, kvlQuantify... successfully generated the nonPartialVolumeStats files and everything worked fine.

I didn't see any threads with this solution, and only one or two that mentioned the problem (http://bit.ly/1vHbV5K), so I thought I'd offer it up in case it could be addressed in a future release.

Cheers, C.P. Frost

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