Thank you Cornelius! Yes I figured that after I sent the question (how
silly of me!)
Andreas was saying that your way of doing this is more convenient. I
wondered what is the difference between running the command you
recommended:
i in "a b c"; do feat $i.fsf; done
and the command that Andreas recommended:
./reem.txt
Where reem.txt would contain all the subjects' *.fsf files ?
I'm sure this is just another silly question but I'd love to understand!
Sorry to be such a bother!
Regards
Reem
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
Behalf Of Cornelius Werner
Sent: Thursday, September 23, 2010 11:37 AM
To: [log in to unmask]
Subject: Re: [FSL] AW: [FSL] AW: multiple inputs in FEAT using 3 column
format
Hi Reem,
since you were worried about results being overwritten: default FEAT
behavior is to create a new directory with an appended "+" if a
directory with an equal name is detected (i.e., A.feat, A+.feat,
A++.feat and so on). As this can be cumbersome during later steps, make
sure that you specify an individual output dir for each subject ("Data"
tab) along with individual 4d and structural data etc.
Glad I could help - usually it's me asking the silly questions ;-))
Cheers,
Cornelius
Am 22.09.2010 um 08:29 schrieb Andreas Bartsch:
> Hi Reem,
>
>> ...save that as design.fsf for that subject
> Yes.
>> make it executable then
> Not really. Your script needs to be executable.
> Assume you generate 4 *.fsf files for 4 of your subjects A-D. If you
don't have any knowledge of scripting you can generate a plain text
file, lets say 'reem.txt' which contains
> feat A.fsf
> feat B.fsf
> feat C.fsf
> feat D.fsf
> Make this file executable:
> chmod 777 reem.txt
> and do:
> ./reem.txt
> This will run feat using your 4 design.fsf's. The data (say A.nii.gz
to D.nii.gz) and *.fsf files are assumed to be stored in the directory
where reem.txt resides (you don't need the txt ending btw). The outputs
will also be there A.feat etc. Thus, nothing is overwritten.
Alternatively (and much more conveniently) you can use the scripting
Cornelius has suggested.
> Best,
> Andreas
>
> ________________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag
von Reem Jan [[log in to unmask]]
> Gesendet: Mittwoch, 22. September 2010 06:20
> An: [log in to unmask]
> Betreff: Re: [FSL] AW: multiple inputs in FEAT using 3 column format
>
> Hi Andreas and/or Cornelius
>
> Sorry in advance about the unintelligent questions. Could I just
clarify
> that I'm understanding you correctly, so in order to make the
design.fsf
> files for each subject, I can use the FEAT Gui to make the design.fsf
> but change the following for each subject:
> 1. Functional 4D data
> 2. Onset files
> 3. Main structural
> Then save that as design.fsf for that subject, make it executable then
> I'd need to run all subjects from the command line?
>
> I'm just confused as to where all the outputs are going to be stored
and
> whether all .fsf files should be saved in the same folder.. I don't
want
> to set it up wrong and have each subject's FEAT overwrite the previous
> subject's?
>
> Thanks for all your help :)
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Andreas Bartsch
> Sent: Monday, September 20, 2010 7:21 PM
> To: [log in to unmask]
> Subject: [FSL] AW: multiple inputs in FEAT using 3 column format
>
> Hi Reem,
>
> unfortuantely, the data / runs you load into the Feat gui must use the
> same model. But you can script running multiple seperate *.fsf files
> (which all have to be executed by feat from command line which you can
> save in a text file - just don't forget to make that executable by
> chmod'ing).
> Hope all is well, cheers-
> Andreas
> ________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag
von
> Reem Jan [[log in to unmask]]
> Gesendet: Montag, 20. September 2010 00:52
> An: [log in to unmask]
> Betreff: [FSL] multiple inputs in FEAT using 3 column format
>
> Dear FSLers
>
> I would like to run multiple subject First Level Analyses in FEAT. I
> know I can load multiple inputs into the FEAT GUI, however, when it
> comes to the model specification I'm not sure how to load multiple
.dat
> onset files (I use a Custom 3-column format). Could someone please let
> me know how I can do this?
>
> Many thanks
> Reem
>
>
>
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