Hi Matthew,
Yes, I have attached the batch script design.fsf, as well as an individual subject's design.fsf . Please let me know if you need anything else!
To refresh, when I open from the GUI and hit "Go" for this participant, it seems to run without issue. The same for when I type from the command line, "feat design.fsf". Again, I am wondering if the NVOL wildcard in the batch script is problematic for the design file (NVOL=`fslnvols $FUNCDATA`), and if so, how I can run a batch script where the number of volumes for each functional run may slightly vary per subject?
Thank you again,
Erin
--------------------------------
Hi Erin - can you load your design into the FEAT GUI and then save it to (e.g) design2.fsf and send me that file?
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 22 Nov 2017, at 15:52, Erin W. <[log in to unmask]> wrote:
>
> Sorry, may have missed that! Reran again with one of the same errors reported initially:
>
> [edub@login1 run1.feat]$ feat_model design
> terminate called after throwing an instance of 'NEWMAT::ProgramException'
> Aborted
>
> Thanks, Matthew!
> Erin
>
> --------------------------------
> Hi Erin,
> Can I just double check that you ran:
> feat_model design ( with an underscore connecting feat_model )
>
> and not
>
> feat model design?
>
> Kindest Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
>> On 21 Nov 2017, at 17:45, Erin W. <[log in to unmask]> wrote:
>>
>> Thank you for your help, Matthew!
>>
>> Yes, the 6_MID_AP.nii.gz file has 248 vols. (I just confirmed this with fslhd as well.)
>>
>> When I run the "feat_model design" within the failed .feat folder, I receive the following error:
>>
>> grep: /proj/dichterlab/BATA/Analysis/MID/Prestats_1stLev/BA0047/BA0047_V1/antic/run1.feat/model.fsf: No such file or directory
>> while executing
>> "exec sh -c "grep -a 'fmri(inmelodic)' $filename | tail -n 1 | awk '{ print \$3 }'" "
>> (procedure "feat5:load" line 5)
>> invoked from within
>> "feat5:load -1 1 ${fsfroot}.fsf"
>> (file "/nas/longleaf/apps/fsl/5.0.10/fsl/bin/feat" line 309)
>>
>>
>> Best,
>> Erin
>>
>> ------------------------------
>> Hello,
>> Can you confirm how many volumes
>>
>> /proj/dichterlab/BATA/Data/Func/BA0047/BA0047_V1/6_MID_AP
>>
>> has? Also if you just run
>>
>> feat_model design
>>
>> in the FEAT directory which fails, do you get any extra error messages?
>>
>> Kind Regards
>> Matthew
>>
>>
>> --------------------------------
>> Dr Matthew Webster
>> FMRIB Centre
>> John Radcliffe Hospital
>> University of Oxford
>>
>>> On 20 Nov 2017, at 21:26, Erin W. <[log in to unmask]> wrote:
>>>
>>> Hi,
>>>
>>> I am receiving a similar error message when attempting to run a batch script and unable to determine the cause.
>>>
>>> Errors as follows:
>>>
>>> "child killed: SIGABRT
>>> while executing
>>> "fsl:exec "${FSLDIR}/bin/feat_model design" $fmri(featModelOpts) -N feat0_model -l logs "
>>> (procedure "firstLevelMaster" line 43)
>>> invoked from within
>>> "firstLevelMaster $session"
>>> invoked from within
>>> "if { $done_something == 0 } {
>>>
>>> if { ! $fmri(inmelodic) } {
>>> if { $fmri(level) == 1 } {
>>> for { set session 1 } { $session <= $fmri(mult..."
>>> (file "/nas/longleaf/apps/fsl/5.0.10/fsl/bin/feat" line 390)
>>> /bin/cp /proj/dichterlab/BATA/Analysis/MID/Prestats_1stLev/BA0047/BA0047_V1/antic/FEAT_run1.fsf design.fsf
>>>
>>> /nas/longleaf/apps/fsl/5.0.10/fsl/bin/feat_model design"
>>>
>>>
>>> "terminate called after throwing an instance of 'NEWMAT::ProgramException'
>>>
>>> FATAL ERROR ENCOUNTERED:
>>> COMMAND:
>>> /nas/longleaf/apps/fsl/5.0.10/fsl/bin/feat_model design
>>> ERROR MESSAGE:
>>> child killed: SIGABRT
>>> END OF ERROR MESSAGE"
>>>
>>>
>>> When I load the design.fsf file for a given participant, all paths appear correctly and it runs without error from the GUI.
>>>
>>> The only thing that I can possibly think of is that in the template.fsf file (attached), I list "Total Number of Volumes" as "NVOL", which in my batch script uses fslnvols to count the number of volumes (because they may slightly vary per person).
>>>
>>> In the script it is: NVOL=`fslnvols $FUNCDATA` (when I echo, there are no errors)
>>>
>>> Any help is appreciated!
>>>
>>> Best,
>>> Erin
>>> <template.fsf><design.fsf>
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