Hi,
Ah, I think this is due to the sensitivity of the brainstem segmentation to where the inferior cutoff of the FOV is. This is an intermittent bug that we have yet to fix (as it is quite infrequent). The best solution for you in this case would be to use run_first_all yourself, but give it a structure list that omits the brainstem.
All the best,
Mark
On 7 Jan 2013, at 14:49, Gillian Cooke <[log in to unmask]> wrote:
> Hi Mark,
>
> Thanks for your response. I checked the first log files and found 2 errors:
>
>
> /usr/local/fsl/bin/run_first: line 164: 85761 Segmentation fault: 11 ${FSLDIR}/bin/first -i $image -l $trmat -m $model -k $outname -n $modes $verbose $comExtras
>
> and
>
> Image Exception : #22 :: ERROR: Could not open image first_results/T1_first-BrStem_corr
> terminate called throwing an exception/bin/sh: line 1: 86404 Abort trap: 6 /usr/local/fsl/bin/fslmerge -t first_results/T1_first_all_fast_firstseg first_results/T1_first-L_Accu_corr first_results/T1_first-L_Amyg_corr first_results/T1_first-L_Caud_corr first_results/T1_first-L_Hipp_corr first_results/T1_first-L_Pall_corr first_results/T1_first-L_Puta_corr first_results/T1_first-L_Thal_corr first_results/T1_first-R_Accu_corr first_results/T1_first-R_Amyg_corr first_results/T1_first-R_Caud_corr first_results/T1_first-R_Hipp_corr first_results/T1_first-R_Pall_corr first_results/T1_first-R_Puta_corr first_results/T1_first-R_Thal_corr first_results/T1_first-BrStem_corr
> Image Exception : #22 :: ERROR: Could not open image first_results/T1_first-BrStem_first
> terminate called throwing an exception/bin/sh: line 1: 86405 Abort trap: 6 /usr/local/fsl/bin/fslmerge -t first_results/T1_first_all_fast_origsegs first_results/T1_first-L_Accu_first first_results/T1_first-L_Amyg_first first_results/T1_first-L_Caud_first first_results/T1_first-L_Hipp_first first_results/T1_first-L_Pall_first first_results/T1_first-L_Puta_first first_results/T1_first-L_Thal_first first_results/T1_first-R_Accu_first first_results/T1_first-R_Amyg_first first_results/T1_first-R_Caud_first first_results/T1_first-R_Hipp_first first_results/T1_first-R_Pall_first first_results/T1_first-R_Puta_first first_results/T1_first-R_Thal_first first_results/T1_first-BrStem_first
> Image Exception : #22 :: ERROR: Could not open image first_results/T1_first_all_fast_origsegs
> Aborted
>
> From what I can gather it is perhaps a segmentation problem, difficulty with the Brain Stem, which is needed to create the origsegs file perhaps?
>
> Best wishes,
> Gillian
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