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FSL  June 2012

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Subject:

Re: Please help- template matching after melöodic

From:

Benjamin Wagner <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 8 Jun 2012 15:01:54 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (148 lines)

About the only other thing I could suggest is trying setenv as opposed to set:

setenv img1 home/kami/testMelodic/test/img1.nii.gz

or

export img1=home/kami/testMelodic/test/img1.nii.gz

Best,
Ben

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of kambiz rakhshan
Sent: Friday, June 08, 2012 10:34 AM
To: [log in to unmask]
Subject: Re: [FSL] Please help- template matching after melöodic

Dear Ben,

Thanks very much for your reply!

That is exactly what I did, but please the problem persist, see below:

kami@kami-Z800-Ubuntu:~/testMelodic/test$ set img1=home/kami/testMelodic/test/img1.nii.gz

kami@kami-Z800-Ubuntu:~/testMelodic/test$ set img2=home/kami/testMelodic/test/img2.nii.gz

kami@kami-Z800-Ubuntu:~/testMelodic/test$ set mask=home/kami/testMelodic/test/mask.nii.gz

kami@kami-Z800-Ubuntu:~/testMelodic/test$ pearcorr
img1: Undefined variable.
img2: Undefined variable.
img1: Undefined variable.

I really don't know why it is not working and I would highly appreciate if you help me!
/kami



--- On Fri, 6/8/12, Benjamin Wagner <[log in to unmask]> wrote:

> From: Benjamin Wagner <[log in to unmask]>
> Subject: Re: [FSL] Please help- template matching after melöodic
> To: [log in to unmask]
> Date: Friday, June 8, 2012, 8:40 AM
> Hello Kami,
> 
> Please replace the #!.  It is correct for the #! to start a script 
> file.  The script is looking for variables to be defined ahead of time 
> and not on the command line.  Depending on what shell you are using 
> you should
> issue:
> 
> set img1=/path/to/some/image1.nii.gz
> set img2=/path/to/some/image2.nii.gz
> set mask=/path/to/some/mask.nii.gz
> pearcorr
> 
> Ben
> 
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On 
> Behalf Of kambiz rakhshan
> Sent: Friday, June 08, 2012 9:08 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Please help- template matching after melöodic
> 
> Thanks,
> but even after removing the hass the program goes to the following 
> line which makes me uncertain about what should I
> do:
> 
> kami-Z800-Ubuntu:~>
> 
> when I enter pearcorr (the name of the program), it just show me 
> aging:
> 
> kami-Z800-Ubuntu:~>
> 
> I don't know really what should I do, and I am really stuck!
> Any help will be highly appreciated!
> 
> Kami
> 
> 
> 
> --- On Fri, 6/8/12, Christine Zakrzewski <[log in to unmask]>
> wrote:
> 
> > From: Christine Zakrzewski <[log in to unmask]>
> > Subject: Re: [FSL] Please help- template matching after
> melöodic
> > To: [log in to unmask]
> > Date: Friday, June 8, 2012, 4:12 AM
> > 
> > 
> > 
> > 
> > at first glance, your shebang is commented out.
> > #!/bin/csh
> >  The shebang tells shell what language to use,
> !/bin/csh. the hash
> > mark tells the shell to ignore this line, when
> executing script.
> > hope this is helpful.
> > christine
> >  
> > >
> > Date: Thu, 7 Jun 2012 15:03:39 -0700
> > > From: [log in to unmask]
> > > Subject: [FSL] Please help- template matching
> after
> > melöodic
> > > To: [log in to unmask]
> > > 
> > > Dear all,
> > > 
> > > I am using the code written by Michael to match
> my
> > resting state network with the one reported in the
> Smith PNAS
> > paper.However, when I run the code(I named it
> pearcorr;see attach), I
> > get some complains about non-defined img1(twice), img2.
> The attach is
> > the code that I used. My knowledge of Linux is very
> little, so I will
> > highly appreciate if someone let me know how shoud I
> run the command.
> > > Many thanks!
> > > 
> > > my commend in the terminal:
> > > 
> > > pearcorr -img1 img1.nii.gz -img2 img2.nii.gz
> -mask
> > mask.nii.gz
> > > 
> > > however:
> > > img1: Undefined variable.
> > > img2: Undefined variable.
> > > img1: Undefined variable.
> > > Kami
> >     
>         
>           
>   
> >
>

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