Also, a suggestion that has been offered by Mark Jenkinsom in the past is to add duplicates of the lasso at inferior slice, in the event that it's failing due to the FOV not including the expected amount of the brainstem. I've never done this personally as I generally always exclude the brainstem.

On Thursday, November 21, 2013, Niels Bergsland wrote:

FIRST is failing on segmenting the brain stem for these cases (at least for the case in which you provided the logs below). If you aren't interested in the brain strm, you can exclude it by specifying only those in which you are interested in by using the -a option to run_first_all. You can get slightly different results on other structures due to he boundary correction applied. So others may disagree and say it's not necessary, but I would probably re-run all cases with ye Brian stem excluded.

On Wednesday, November 20, 2013, Michael Kranz wrote:
Hi,

Although FIRST was successful in outputting the *_all_fast_origsegs.nii.gz and *_all_fast_firsteg.nii.gz volumes, a few subjects did not have these volumes.

For these subjects, the rest of the output was segmented successfully (i.e. bvars and vtk and standardized volumes). Additionally, the registrations were successful.

The errors received do not seem to tell me much about the nature of the error (only that it does not exist)…

/usr/local/fsl/bin/run_first: line 164: 71885 Segmentation fault: 11 ${FSLDIR}/bin/first -i $image -l $trmat -m $model -k $outname -n $modes $verbose $comExtras

Image Exception : #22 :: ERROR: Could not open image s41-BrStem_corr
terminate called throwing an exception/bin/sh: line 1: 71934 Abort trap: 6 /usr/local/fsl/bin/fslmerge -t s41_all_fast_firstseg s41-L_Accu_corr s41-L_Amyg_corr s41-L_Caud_corr s41-L_Hipp_corr s41-L_Pall_corr s41-L_Puta_corr s41-L_Thal_corr s41-R_Accu_corr s41-R_Amyg_corr s41-R_Caud_corr s41-R_Hipp_corr s41-R_Pall_corr s41-R_Puta_corr s41-R_Thal_corr s41-BrStem_corr

Image Exception : #22 :: ERROR: Could not open image s41-BrStem_first
terminate called throwing an exception/bin/sh: line 1: 71935 Abort trap: 6 /usr/local/fsl/bin/fslmerge -t s41_all_fast_origsegs s41-L_Accu_first s41-L_Amyg_first s41-L_Caud_first s41-L_Hipp_first s41-L_Pall_first s41-L_Puta_first s41-L_Thal_first s41-R_Accu_first s41-R_Amyg_first s41-R_Caud_first s41-R_Hipp_first s41-R_Pall_first s41-R_Puta_first s41-R_Thal_first s41-BrStem_first

Image Exception : #22 :: ERROR: Could not open image s41_all_fast_origsegs
Aborted

Thanks,
Mike Kranz

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Michael Kranz
Graduate Research Assistant |Beckman Institute University of Illinois
314-323-1329

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Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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(716) 859-7677