hi, I don't have matlab in my freesurfer path, instead I download Matlab Runtime as described in following link:

https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime

as my freesurfer version is " freesurfer-linux-centos6_x86_64_stable_pub-v6", so I download:

curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bLinux.tar.gz" -o "runtime.tar.gz"

and then unpack it. now MCR.V8 is in my freesurfer path, but still fcseedcor and of course mkanalysis-sess commands, doesn't work. and bellow massage is appear in my terminal.

------- matlab output --------------------

> matlab: Command not found.

How can I fix it and obtain connectivity matrix with fcseedcor?

thank you with your help ,

sara

-----Original Message-----
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
To: Sara Jafakesh <S.Jafakesh@sutech.ac.ir>, "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Date: Mon, 10 Dec 2018 23:46:58 +0000
Subject: Re: Fwd: fcseedcor output

Is matlab in your path? What happens when you run
which matlab

On 12/10/2018 06:12 PM, Sara Jafakesh wrote:
>
>         External Email - Use Caution
>
>
> -----Original Message-----
> From: "Sara Jafakesh" <S.Jafakesh@sutech.ac.ir>
> To: freesurfer@nmr.mgh.harvard.edu
> Cc: DGREVE@mgh.harvard.edu
> Date: Sat, 08 Dec 2018 22:25:20 +0330
> Subject: Fwd: fcseedcor output
>
>
> -----Original Message-----
> From: "Sara Jafakesh" <S.Jafakesh@sutech.ac.ir>
> To: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu >
> Date: Sat, 08 Dec 2018 12:21:06 +0330
> Subject: Re: fcseedcor output
>
> Dear Greve
> I send the entire email chain:
> I think some thing wrong with my matlab setting, It is not
> compatible with my freesurfer I guess, but I dont know how can
> I compatible matlab with freesurfer.
> best..
> Can? you send the full terminal output?
> On 12/05/2018 01:25 AM, Sara Jafakesh wrote:
> >
> > ????????External Email - Use Caution
> >
> >
> > Dear freesurfer experts,
> > I want to calculate corrolation between two seeds with
> > freesurfer-linux-centos6_x86_64_stable_pub-v6 .after using
> > fcseed-config and fcseed-sess, I used fcseedcor. the
> command
> > that I trying to run is as follow:
> > fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed
> > lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg
> mcprextreg
> > 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat
> > but the output of fcseedcor is not dat file ( the
> > connectivity matrix for my result 2*2 matrix) as it
> has been
> > explained in the fcssedcor help. the output is just
> the log
> > file named seedcor2.dat.log. although it has been done
> > without error.
> > I really dont know what is the problem.
> > I would be grateful if you could help me.
> > best regards,
> > sara
> hi sara, can you include the entire email chain so that I can
> see the context?
> On 12/7/18 4:19 PM, Sara Jafakesh wrote:
> External Email - Use Caution
> Dear Dr.GREVE ,
> thank you for your reply
> my full terminal output is:
> [user at localhost subjects]$ fcseedcor -s subj1 -fsd rest
> -seed lh-seed2.dat
> -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg
> mcprextreg 6 -hpf
> .001 -lpf .1 -nskip 6 -o seedcor2.dat
> Sat Dec 1 18:05:11 IRST 2018
> setenv SUBJECTS_DIR /home/user/freesurfer/subjects
> cd /home/user/freesurfer/subjects
> /home/user/freesurfer/fsfast/bin/fcseedcor -s subj1 -fsd rest
> -seed
> lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat
> 5 -xreg
> mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $
> Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP Tue
> May 10 17:27:01
> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
> ------- matlab output --------------------
> matlab: Command not found.
> Started at Sat Dec 1 18:05:11 IRST 2018
> Ended at Sat Dec 1 18:05:12 IRST 2018
> Fcseedcor-Run-Time-Sec 1
> Fcseedcor-Run-Time-Hours 0.00
> fcseedcor Done
> best,
> sara
>
> -----Original Message-----
> From: "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu>
> To: Sara Jafakesh <S.Jafakesh@sutech.ac.ir>,
> " 87fc6eef-18d0-2f7d-99f5-eb8a79707c5c@mgh.harvard.edu"
> < 87fc6eef-18d0-2f7d-99f5-eb8a79707c5c@mgh.harvard.edu>
> Cc: " freesurfer@nmr.mgh.harvard.edu"
> < freesurfer@nmr.mgh.harvard.edu>
> Date: Fri, 7 Dec 2018 22:33:49 +0000
> Subject: Re: fcseedcor output
>
> hi sara, can you include the entire email chain so that I
> can see the context?
>
> On 12/7/18 4:19 PM, Sara Jafakesh wrote:
>>         External Email - Use Caution
>> Dear Dr.GREVE ,
>> thank you for your reply
>> my full terminal outpou is :
>> [user@localhost subjects]$ fcseedcor -s subj1 -fsd rest
>> -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5
>> -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1
>> -nskip 6 -o seedcor2.dat
>> Sat Dec 1 18:05:11 IRST 2018
>>
>> setenv SUBJECTS_DIR /home/user/freesurfer/subjects
>> cd /home/user/freesurfer/subjects
>> /home/user/freesurfer/fsfast/bin/fcseedcor -s subj1 -fsd
>> rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5
>> -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1
>> -nskip 6 -o seedcor2.dat
>>
>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>> $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $
>> Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP
>> Tue May 10 17:27:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>> ------- matlab output --------------------
>> matlab: Command not found.
>>
>> Started at Sat Dec 1 18:05:11 IRST 2018
>> Ended   at Sat Dec 1 18:05:12 IRST 2018
>> Fcseedcor-Run-Time-Sec 1
>> Fcseedcor-Run-Time-Hours 0.00
>>
>> fcseedcor Done
>> best,
>> sara
>
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