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&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." <dgr...@mgh.harvard.edu> > To: Sara Jafakesh <s.jafak...@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.jafak...@sutech.ac.ir > <mailto:S.Jafakesh%40sutech.ac.ir>> > > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer%40nmr.mgh.harvard.edu> > > Cc: dgr...@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.jafak...@sutech.ac.ir > <mailto:S.Jafakesh%40sutech.ac.ir>> > > To: "Greve, Douglas N.,Ph.D." <dgr...@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." > <dgr...@mgh.harvard.edu <mailto:DGREVE%40mgh.harvard.edu>> > > To: Sara Jafakesh <s.jafak...@sutech.ac.ir > <mailto:S.Jafakesh%40sutech.ac.ir>>, > > > "87fc6eef-18d0-2f7d-99f5-eb8a79707...@mgh.harvard.edu > <mailto:87fc6eef-18d0-2f7d-99f5-eb8a79707c5c%40mgh.harvard.edu>" > > > <87fc6eef-18d0-2f7d-99f5-eb8a79707...@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. If you believe this e-mail was sent to you in > > error and the e-mail > > contains patient information, please contact the > Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline > <http://www.partners.org/complianceline> . If the e-mail was > > sent to you in error > > but does not contain patient information, please contact > > the sender and properly > > dispose of the e-mail. > > >
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