Hi Amelia,
Would you be able to upload the results of your analysis (the entire
.feat directory) so I can take a look?
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=76071220381FA9CD1C
Cheers,
Paul
On 23/07/2019, Amelia Couture <[log in to unmask]> wrote:
> Hi Paul,
>
> Thank you for the suggestion that my brain data and mask may not be in the
> same space--I ran the analyses on the group-level data, and this fixed the
> error message.
>
> While I no longer received an error, when I check the results I still see
> activation outside of the masked region. Do you have any ideas of why this
> may be occurring? The analysis reports that Z-stat images were masked with
> my mask file before thresholding, so I'm not sure what's going on.
>
> Any suggestions would be much appreciated!
> Amelia
>
> On Fri, Jul 19, 2019 at 8:00 AM Amelia Couture <[log in to unmask]> wrote:
>
>> Hi Paul,
>>
>> Thank you for the clarification! I will make sure my data and
>> pre-threshold mask are in the same space and re-try the analyses after
>> that. Thanks again--I really appreciate your help.
>>
>> Best,
>> Amelia
>>
>> On Fri, Jul 19, 2019 at 7:48 AM paul mccarthy <[log in to unmask]>
>> wrote:
>>
>>> Hi Amelia,
>>>
>>> Regardless of whether you are running a first-level or group-level
>>> analysis, the pre-threshold mask must be defined in the same space as
>>> your data. You will need to transform your mask into the native
>>> functional space for your subject (or for each of your subjects).
>>>
>>> Cheers,
>>>
>>> Paul
>>>
>>> On 19/07/2019, Amelia Couture <[log in to unmask]> wrote:
>>> > Hi Paul,
>>> >
>>> > Thank you for your response--this is a first-level analysis. Would it
>>> > be
>>> > appropriate to run the mask at the group-level analysis instead?
>>> >
>>> > Best,
>>> > Amelia
>>> >
>>> > On Fri, Jul 19, 2019 at 1:08 AM paul mccarthy
>>> > <[log in to unmask]>
>>> > wrote:
>>> >
>>> >> Hi Amelia,
>>> >>
>>> >> Is this a first-level or group-level analysis?
>>> >>
>>> >> My only thought is that your mask (which is defined in MNI152 space)
>>> >> may not be in the same space as your data (which may be in subject
>>> >> functional space)
>>> >>
>>> >> Cheers,
>>> >>
>>> >> Paul
>>> >>
>>> >> On 16/07/2019, Amelia Couture <[log in to unmask]> wrote:
>>> >> > Hello,
>>> >> >
>>> >> > It's been a few days and I still haven't been able to figure this
>>> out.
>>> >> Does
>>> >> > anyone have any ideas?
>>> >> >
>>> >> > I've been working on analyses using a ROI mask, and have been
>>> >> > running
>>> >> into
>>> >> > some difficulties. When I add in my mask file to the pre-threshold
>>> >> masking
>>> >> > field in the GUI, I get the following error:
>>> >> >
>>> >> > /usr/local/fsl/bin/fsl_sub -T 119 -l logs -N feat4_post -j 15012
>>> >> > /usr/local/fsl/bin/feat *file path to design.fsf* -D *File path to
>>> >> > Subject001_Run1.feat* -poststats 0
>>> >> > child killed: SIGABRT
>>> >> > while executing
>>> >> > "if { [ catch {
>>> >> >
>>> >> > for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>>> >> > switch -- [ lindex $argv $argindex ] {
>>> >> >
>>> >> > -I {
>>> >> > incr arginde..."
>>> >> > (file "/usr/local/fsl/bin/feat" line 312)
>>> >> >
>>> >> > FATAL ERROR ENCOUNTERED:
>>> >> > COMMAND:
>>> >> > /usr/local/fsl/bin/fsl_sub -T 119 -l logs -N feat4_post -j 15012
>>> >> > /usr/local/fsl/bin/feat *File path to design.fsf* -D *File path to
>>> >> > Subject001_Run1+.feat* -poststats 0
>>> >> > ERROR MESSAGE:
>>> >> > child process exited abnormally
>>> >> > END OF ERROR MESSAGE
>>> >> >
>>> >> > Everything works correctly when I run the same analysis without the
>>> >> > mask.
>>> >> > I've attached the file that I'm uploading for the mask in case
>>> >> > that's
>>> >> > helpful to see.
>>> >> >
>>> >> > Thanks!
>>> >> > Amelia
>>> >> > --
>>> >> > Amelia Couture Bue
>>> >> > Ph.D Candidate
>>> >> > Department of Communication Studies
>>> >> > University of Michigan
>>> >> > (she/her/hers)
>>> >> >
>>> >> >
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>>> >> >
>>> >>
>>> >>
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>>> >>
>>> >
>>> >
>>> > --
>>> > Amelia Couture Bue
>>> > Ph.D Candidate
>>> > Department of Communication Studies
>>> > University of Michigan
>>> > (she/her/hers)
>>> >
>>> > ########################################################################
>>> >
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>>> >
>>>
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>>>
>>
>>
>> --
>> Amelia Couture Bue
>> Ph.D Candidate
>> Department of Communication Studies
>> University of Michigan
>> (she/her/hers)
>>
>
>
> --
> Amelia Couture Bue
> Ph.D Candidate
> Department of Communication Studies
> University of Michigan
> (she/her/hers)
>
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>
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