Hi Martin,
Well spotted! This will be fixed for the next release.
Thanks!
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
On 7 Jun 2018, at 14:21, Martin Craig <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi, I think there is a minor bug at the very end of FSL_ANAT. I am using version 5.0.11 and in the final step (SUB-CORTICAL STRUCTURE SEGMENTATION) there is the following:
echo "$FSLDIR/bin/fsl_sub -T 1 -j $FIRSTID imcp first_results/${T1}_first_all_fast_firstseg.${ext} ${T1}_subcort_seg.${ext}" >> $LOGFILE
$FSLDIR/bin/fsl_sub -T 1 -j $FIRSTID imcp first_results/${T1}_first_all_fast_firstseg.${ext} ${T1}_subcort_seg.${ext}
The ${ext} variable is not defined (and not necessary as far as I can tell - if you remove it, imcp figures out the extension itself), however it causes the command to fail because the file extension is not recognized.
Since this is literally the last real command in the script, it doesn't have much impact, however it does cause fsl_anat to exit with status 1 which was then causing another of my scripts to fail!
I can work around it easily, but looks like an straightforward fix for the next release.
Cheers,
Martin
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