Hi all,

In our efforts to take our 5.2 edits to 5.3 we tried the command below (in the attached thread), but we also tried the command

recon-all –s [subject-d] -autorecon2 –autorecon3

and those jobs are also running for some time but then crashing with the same error complaining that lh.BA1.thresh.label does not exist.

We are on RedHat 5.2, running the 2.6.18-19.1.13.e15 kernel and using the BASH environment. We are using the release 5.3.0-centos04.

The log and other relevant files can be found at:

http://www-personal.umich.edu/~rcwelsh/bug/recon-all.cmd

http://www-personal.umich.edu/~rcwelsh/bug/recon-all.log

http://www-personal.umich.edu/~rcwelsh/bug/recon-all.env

http://www-personal.umich.edu/~rcwelsh/bug/recon-all.error

I've dug into the code and see that the block of code in recon-all was introduced going from 5.2 to 5.3.

# generate .thresh labels foreach balabel (BA1 BA2 BA3a BA3b BA4a BA4p BA6 BA44 BA45 V1 V2 MT) set cmd=(mri_label2label \ --srcsubject fsaverage \ --srclabel $SUBJECTS_DIR/fsaverage/label/${hemi}.${balabel}.thresh.label \ --trgsubject $subjid \ --trglabel ./${hemi}.${balabel}.thresh.label \ --hemi ${hemi} \ --regmethod surface) echo "\n $cmd \n"|& tee -a $LF |& tee -a $CF if($RunIt) $fs_time $cmd |& tee -a $LF if($status) goto error_exit; end # balabel

This is what is throwing the error.

Hopefully, we can get this resolved soon.

(Also as a side note in the version 5.2 we had to comment out the reference to perirhinal in the first "foreach balabel" loop as perirhinal was giving a bug)

Thanks,

-Robert

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