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-----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:

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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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