External Email - Use Caution
-----Original Message-----
From: "Sara Jafakesh" <s.jafak...@sutech.ac.ir>
To: freesurfer@nmr.mgh.harvard.edu
Cc: dgr...@mgh.harvard.edu
Date: Sat, 08 Dec 2018 22:25:20 +0330
Subject: Fwd: fcseedcor output
-----Original Message-----
From: "Sara Jafakesh" <s.jafak...@sutech.ac.ir>
To: "Greve, Douglas N.,Ph.D." <dgr...@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." <dgr...@mgh.harvard.edu>
To: Sara Jafakesh <s.jafak...@sutech.ac.ir>,
"87fc6eef-18d0-2f7d-99f5-eb8a79707...@mgh.harvard.edu"
<87fc6eef-18d0-2f7d-99f5-eb8a79707...@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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