Hi Mark,
Looks like you may have missed that Nele is already using the -s
option and is only segmenting the accumbens.
Nele, first off, you don't need two separate run_first_all calls, you
can use a single call and specify the left and right accumbens to be
segmented as a comma separated list. (e.g. run_first_all -s
L_Accu,R_Accu -i wmR_nback_${i}* -o R_nback_NA${i} ) This is not the
reason it's failing but just wanted to point it out.
However, I have occasionally run into problems with accumbens
segmentation. If you can make the structural images available for some
of the failed cases, I'm happy to take a look.
Best,
Niels
On Thu, Nov 27, 2014 at 4:36 PM, Mark Jenkinson
<[log in to unmask]> wrote:
> Hi,
>
> One thing that makes FIRST crash sometimes is a small FOV in the inferior direction when it attempts to do brainstem segmentation. Try running one of the problematic subjects but with a restricted set of structures (via the -s option) that excludes the brainstem. If this works then the problem is most likely to be the brainstem segmentation and you can just run your script and specifically exclude the brainstem (by listing all other structures with the -s option). If it still causes problems on other structures (not the brainstem) then let us know.
>
> All the best,
> Mark
>
>
>> On 27 Nov 2014, at 10:58, Nele De Witte <[log in to unmask]> wrote:
>>
>> Dear experts,
>>
>> I ran FIRST in about 50 participants, and it worked perfectly for most of them. However 8 participants failed.
>>
>> this was the script:
>>
>> #!/bin/bash
>>
>> for i in 6_ 7_ 8_ 9_ 10_ 11_ 16_ 17_ 18_ 19_ 20_ 21_ 22_ 24_ 25_ 26_ 27_ 29_ 30_ 31_ 33 34 35 37 39 40 41 42 50 52 53 56 61 68 69 70 72 73 75 80 82 83 85 87 88 89 90 92 93 94 96 97;
>> do
>> run_first_all -s L_Accu -i wmR_nback_${i}* -o R_nback_NA${i};
>> run_first_all -s R_Accu -i wmR_nback_${i}* -o R_nback_NA${i};
>>
>> done
>>
>> And in the log of the failes ones I found
>> terminate called after throwing an instance of 'NEWMAT::SingularException'
>> /usr/local/fsl/bin/run_first: line 164: 19713 Aborted (core dumped) ${FSLDIR}/bin/first -i $image -l $trmat -m $model -k $outname -n $modes $verbose $comExtras
>>
>> Since the other logs all refer to missing files, I assume that something went wrong in the first step. I've looked at the images of these participants and I see no obvious differences with the structural images of the rest of the group.
>>
>> Does anybody have any ideas as to the cause of this problem?
>>
>> Thank you very much!
>>
>> Nele De Witte
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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