-----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

 

hi, I send the entire email chain:

 

 

 

 

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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