11 Dec
2018
11 Dec
'18
5:12 p.m.
sorry, I don't have a matlab binary for fast_fcseedcor
On 12/11/2018 05:07 PM, Sara Jafakesh wrote:
External Email - Use Caution
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&am..." -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 <mailto:S.Jafakesh%40sutech.ac.ir>> > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer%40nmr.mgh.harvard.edu> > Cc: DGREVE@mgh.harvard.edu <mailto:DGREVE%40mgh.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 <mailto:S.Jafakesh%40sutech.ac.ir>> > To: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu <mailto:DGREVE%40mgh.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 <mailto:DGREVE%40mgh.harvard.edu>> > To: Sara Jafakesh <S.Jafakesh@sutech.ac.ir <mailto:S.Jafakesh%40sutech.ac.ir>>, > "87fc6eef-18d0-2f7d-99f5-eb8a79707c5c@mgh.harvard.edu <mailto:87fc6eef-18d0-2f7d-99f5-eb8a79707c5c%40mgh.harvard.edu>" > <87fc6eef-18d0-2f7d-99f5-eb8a79707c5c@mgh.harvard.edu <mailto:87fc6eef-18d0-2f7d-99f5-eb8a79707c5c%40mgh.harvard.edu>> > Cc: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer%40nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer%40nmr.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 > > The information in this e-mail is intended only for the > person to whom it is > addressed. 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