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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