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		FSL July 2019
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Subject:
Re: Group ICA not generating power spectra and BOLD plots
From:
paul mccarthy <[log in to unmask]>
Reply-To:
FSL - FMRIB's Software Library <[log in to unmask]>
Date:
Tue, 30 Jul 2019 11:45:06 +0100
Content-Type:
text/plain
Parts/Attachments:
text/plain (387 lines)
Hi Ishi,

Could you give the exact command used, the location it was executed
from, and the exact output?

Paul

On 29/07/2019, Ishi Tandon <[log in to unmask]> wrote:
> Hi Paul,
> I tried running dual regression with the on multiple samples except my
> data. The terminal displays an error that drA and drC files not found.
> Though drA and so on files are generated after dual regression. Is there
> something wrong with data?
>
> *Regards,*
>
> *Ishi Tandon*
> *B.tech + M.tech - Cognitive & Neuroscience*
> *Amity University, Rajasthan*
> *contact - +918239259846 ; Email- [log in to unmask]
> <[log in to unmask]>*
>
>
> On Thu, Jul 25, 2019 at 8:37 PM paul mccarthy <[log in to unmask]>
> wrote:
>
>> Hi Ishi,
>>
>> There may be something wrong with the fsl_sub command on your system.
>> Could you try running the modified version of dual_regression attached
>> to this email? You may need to run:
>>
>> chmod a+x /path/to/downloaded/dual_regression
>>
>> before being able to call it
>>
>> Paul
>>
>> On 25/07/2019, Ishi Tandon <[log in to unmask]> wrote:
>> > Hi Paul,
>> > This is what i get on my terminal when I type imglob. Please find the
>> > attached file.
>> > *Regards,*
>> >
>> > *Ishi Tandon*
>> > *B.tech + M.tech - Cognitive & Neuroscience*
>> > *Amity University, Rajasthan*
>> > *contact - +918239259846 ; Email- [log in to unmask]
>> > <[log in to unmask]>*
>> >
>> >
>> > On Wed, Jul 24, 2019 at 5:25 PM paul mccarthy <[log in to unmask]>
>> > wrote:
>> >
>> >> Hi Ishi,
>> >>
>> >> This might be due to an incomplete FSL installation. What happens when
>> >> you type "imglob" (without the quotes) into a terminal?
>> >>
>> >> Paul
>> >>
>> >> On 24/07/2019, Ishi Tandon <[log in to unmask]> wrote:
>> >> > It said creating common masks, running randomise and done dual
>> >> regression.
>> >> > Only three outputs were generated corresponding to it. Total time
>> taken
>> >> was
>> >> > nearly 3 mins.
>> >> > *Regards,*
>> >> >
>> >> > *Ishi Tandon*
>> >> > *B.tech + M.tech - Cognitive & Neuroscience*
>> >> > *Amity University, Rajasthan*
>> >> > *contact - +918239259846 ; Email- [log in to unmask]
>> >> > <[log in to unmask]>*
>> >> >
>> >> >
>> >> > On Wed, Jul 24, 2019 at 1:07 PM paul mccarthy <
>> [log in to unmask]>
>> >> > wrote:
>> >> >
>> >> >> Hi Ishi,
>> >> >>
>> >> >> By "output", I mean what was printed to the terminal when you
>> >> >> called
>> >> >> the dual_regression script.
>> >> >>
>> >> >> Paul
>> >> >>
>> >> >> On 24/07/2019, Ishi Tandon <[log in to unmask]> wrote:
>> >> >> > Following is the output directory that is generated. This is all
>> >> >> > in
>> >> the
>> >> >> > folder called grot.
>> >> >> >
>> >> >> > On Tue, Jul 23, 2019 at 1:44 PM paul mccarthy <
>> >> [log in to unmask]>
>> >> >> > wrote:
>> >> >> >
>> >> >> >> Hi Ishi,
>> >> >> >>
>> >> >> >> Do you get *any* output at all when you run dual regression?
>> >> >> >>
>> >> >> >> Paul
>> >> >> >>
>> >> >> >> On 23/07/2019, Ishi Tandon <[log in to unmask]> wrote:
>> >> >> >> > I don't get any errors on the terminal while i run dual
>> >> >> >> > regression.
>> >> >> But
>> >> >> >> in
>> >> >> >> > the grot folder dr_stage files ain't formed.
>> >> >> >> >
>> >> >> >> > On Mon, Jul 22, 2019 at 9:31 PM Ishi Tandon
>> >> >> >> > <[log in to unmask]>
>> >> >> >> > wrote:
>> >> >> >> >
>> >> >> >> >> Yes you can run dual regression. Do share the output.
>> >> >> >> >> How can I use dual regression to obtain the time courses of
>> each
>> >> >> >> subject?
>> >> >> >> >> I tried to view the time courses through FSLeyes and they
>> >> >> >> >> were
>> >> >> >> >> visible.
>> >> >> >> I
>> >> >> >> >> had big doubt regarding group ICA time series, thanks for
>> >> >> >> >> clearing
>> >> >> >> >> it
>> >> >> >> >> out.
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> On Mon, Jul 22, 2019 at 9:08 PM paul mccarthy
>> >> >> >> >> <[log in to unmask]>
>> >> >> >> >> wrote:
>> >> >> >> >>
>> >> >> >> >>> Hi Ishi,
>> >> >> >> >>>
>> >> >> >> >>> Your group ICA results look fine; the time series and power
>> >> >> >> >>> spectra
>> >> >> >> >>> plots are no longer generated as part of a group ICA report,
>> >> >> >> >>> because
>> >> >> >> >>> group ICA uses an optimisation technique called MIGP which
>> >> >> >> >>> causes
>> >> >> the
>> >> >> >> >>> mixing matrix to no longer reflect the underlying component
>> >> >> >> >>> time
>> >> >> >> >>> courses. Instead, you can use dual regression to get the
>> >> >> >> >>> time
>> >> >> courses
>> >> >> >> >>> for each subject.
>> >> >> >> >>>
>> >> >> >> >>> I can run dual regression on your data without any problem
>> >> >> >> >>> at
>> >> >> >> >>> all
>> >> >> >> >>> -
>> >> >> >> >>> what was output to the terminal when you ran it?
>> >> >> >> >>>
>> >> >> >> >>> Cheers,
>> >> >> >> >>>
>> >> >> >> >>> Paul
>> >> >> >> >>>
>> >> >> >> >>> On 22/07/2019, Ishi Tandon <[log in to unmask]> wrote:
>> >> >> >> >>> > Hi There,
>> >> >> >> >>> > Somehow OxFile was taking longer time than usual. Here are
>> >> >> >> >>> > the
>> >> >> >> >>> > Google
>> >> >> >> >>> Drive
>> >> >> >> >>> > links. This is the test data for 5 subjects. The same
>> >> >> >> >>> > issue
>> >> >> >> >>> > persists.
>> >> >> >> >>> >
>> >> >> >> >>>
>> >> >> >>
>> >> >>
>> >>
>> https://drive.google.com/file/d/1A0RfmJhqktRJ1TUadxE9VFv_ajP_62RW/view?usp=sharing
>> >> >> >> >>> >
>> >> >> >> >>> >
>> >> >> >> >>> >
>> >> >> >> >>> > On Mon, Jul 22, 2019 at 7:56 AM Ishi Tandon
>> >> >> >> >>> > <[log in to unmask]
>> >> >> >> >
>> >> >> >> >>> > wrote:
>> >> >> >> >>> >
>> >> >> >> >>> >> Sure i will do that in a while.
>> >> >> >> >>> >> *Regards,*
>> >> >> >> >>> >>
>> >> >> >> >>> >> *Ishi Tandon*
>> >> >> >> >>> >> *B.tech + M.tech - Cognitive & Neuroscience*
>> >> >> >> >>> >> *Amity University, Rajasthan*
>> >> >> >> >>> >> *contact - +918239259846 ; Email- [log in to unmask]
>> >> >> >> >>> >> <[log in to unmask]>*
>> >> >> >> >>> >>
>> >> >> >> >>> >>
>> >> >> >> >>> >> On Mon, Jul 22, 2019 at 1:18 PM paul mccarthy
>> >> >> >> >>> >> <[log in to unmask]
>> >> >> >> >>> >
>> >> >> >> >>> >> wrote:
>> >> >> >> >>> >>
>> >> >> >> >>> >>> Hi Ishi,
>> >> >> >> >>> >>>
>> >> >> >> >>> >>> Would you be able to zip up the contents of your melodic
>> >> >> >> >>> >>> and
>> >> >> dual
>> >> >> >> >>> >>> regression output directories and upload them to:
>> >> >> >> >>> >>>
>> >> >> >> >>> >>>
>> >> >> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=7594581385A6E05F08
>> >> >> >> >>> >>>
>> >> >> >> >>> >>> so I can take a look?
>> >> >> >> >>> >>>
>> >> >> >> >>> >>> Paul
>> >> >> >> >>> >>>
>> >> >> >> >>> >>> On 21/07/2019, Ishi Tandon <[log in to unmask]>
>> wrote:
>> >> >> >> >>> >>> > There were no errors or warnings displayed by either
>> >> >> >> >>> >>> >
>> >> >> >> >>> >>> > On Sun, Jul 21, 2019 at 5:32 PM paul mccarthy
>> >> >> >> >>> >>> > <[log in to unmask]>
>> >> >> >> >>> >>> > wrote:
>> >> >> >> >>> >>> >
>> >> >> >> >>> >>> >> Hi Ishi,
>> >> >> >> >>> >>> >>
>> >> >> >> >>> >>> >> Were any errors or warnings output by melodic or
>> >> >> >> dual_regression?
>> >> >> >> >>> >>> >>
>> >> >> >> >>> >>> >> Paul
>> >> >> >> >>> >>> >>
>> >> >> >> >>> >>> >> On 21/07/2019, Ishi Tandon <[log in to unmask]>
>> >> wrote:
>> >> >> >> >>> >>> >> > Hi there
>> >> >> >> >>> >>> >> > After running group Ica on  64 subject’s resting
>> >> >> >> >>> >>> >> > fmri
>> >> >> >> >>> >>> >> > data,
>> >> >> >> >>> >>> >> > I
>> >> >> >> >>> >>> >> > didn’t
>> >> >> >> >>> >>> >> > get
>> >> >> >> >>> >>> >> the
>> >> >> >> >>> >>> >> > power spectra and BOLD plots below the components
>> >> >> >> >>> >>> >> > in
>> >> >> >> >>> >>> >> > the
>> >> >> >> >>> >>> >> > report.
>> >> >> >> >>> >>> After
>> >> >> >> >>> >>> >> > running dual regression dr_stage_1, 2 and 3 files
>> were
>> >> >> >> >>> >>> >> > not
>> >> >> >> >>> formed.
>> >> >> >> >>> >>> >> > I am using FSL version 6.0.1. The same problem
>> >> >> >> >>> >>> >> > persisted
>> >> >> >> >>> >>> >> > in
>> >> >> >> >>> >>> >> > both
>> >> >> >> >>> >>> ubuntu
>> >> >> >> >>> >>> >> > 18.04 and macOS 10.14.5 Mojave.
>> >> >> >> >>> >>> >> > Why is that happening?
>> >> >> >> >>> >>> >> >
>> >> >> >> >>> >>> >> >
>> >> >> >> >>> >>>
>> >> >> >> >>>
>> >> >> >>
>> >> ########################################################################
>> >> >> >> >>> >>> >> >
>> >> >> >> >>> >>> >> > To unsubscribe from the FSL list, click the
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>> >> >> >> >>> >>> >> > link:
>> >> >> >> >>> >>> >> >
>> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>> >> >> >> >>> >>> >> >
>> >> >> >> >>> >>> >>
>> >> >> >> >>> >>> >>
>> >> >> >> >>> >>>
>> >> >> >> >>>
>> >> >> >>
>> >> ########################################################################
>> >> >> >> >>> >>> >>
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>> >> >> >> >>> >>> >>
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>> >> >> >> >>> >>> >>
>> >> >> >> >>> >>> >
>> >> >> >> >>> >>> >
>> >> >> >> >>>
>> >> >> >>
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