Sorry for the typo, that should be -s, not -a.
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
>>
>> --
>> Michael Kranz
>> Graduate Research Assistant |Beckman Institute University of Illinois
>> 314-323-1329
>>
>
>
> --
> Niels Bergsland
> Integration Director
> Buffalo Neuroimaging Analysis Center
> 100 High St. Buffalo NY 14203
> [log in to unmask]
> (716) 859-7677
>
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
[log in to unmask]
(716) 859-7677
