Hi Erin,
Just to clarify, the subject design.fsf has been generated from the batch script with no further processing? Also are you invoking FEAT in the same way in the script as in the command line ( feat design.fsf ). Do you have a design.fsf from the feat folder of a subject which has worked succesfully ( via opening in the GUI etc ) and the corresponding design.fsf that was generated by the script?
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 22 Nov 2017, at 22:31, Erin W. <[log in to unmask]> wrote:
>
> 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>
> <BATCH_design.fsf><SUBJ_design.fsf>
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