Hi Ameila,
I don't see any activation outside of your mask region in the
thresholded zstat images (I don't see any activation at all).
Were you by any chance looking at the unthresholded zstat images?
Paul
On 24/07/2019, Amelia Couture <[log in to unmask]> wrote:
> Hi Paul,
>
> Absolutely! I just finished uploading the files, and look forward to
> hearing your ideas. Thanks in advance for taking a look.
>
> Best,
> Amelia
>
> On Wed, Jul 24, 2019 at 12:33 AM paul mccarthy <[log in to unmask]>
> wrote:
>
>> 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)
>> >>> >> >
>> >>> >> >
>> >>>
>> ########################################################################
>> >>> >> >
>> >>> >> > To unsubscribe from the FSL list, click the following link:
>> >>> >> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>> >>> >> >
>> >>> >>
>> >>> >>
>> >>>
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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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>
>
> --
> Amelia Couture Bue
> Ph.D Candidate
> Department of Communication Studies
> University of Michigan
> (she/her/hers)
>
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