permission denied means that you don't have write permission into /Users/dhirjak/freesurfer/matlab/matlab you have to set up a link to a folder that is in your path
On 02/03/2014 05:42 PM, Dusan Hirjak wrote: > Dear Sebastian, > > Im still working on my problem. I tried to put a symbolic link to the > matlab binary and got the following answer: > > bash-3.2$ ln -s /Users/dhirjak/MATLAB_R2013a.app/bin/matlab > /Users/dhirjak/bin/matlab > > ln: /Users/dhirjak/bin/matlab: No such file or directory > > bash-3.2$ ln -s /Users/dhirjak/MATLAB_R2013a.app/bin/matlab > /Users/dhirjak/freesurfer/matlab > > ln: /Users/dhirjak/freesurfer/matlab/matlab: Permission denied > > bash-3.2$ > > > > I also tried to add path in matlab, but it is still not working. > > > What is the problem??? What does it mean "permission denied"??? What > should I do next? > > > Many thanks, > > > > > DH > > > > > > From: [email protected] > > Date: Sun, 26 Jan 2014 16:33:40 +0100 > > To: [email protected] > > CC: [email protected] > > Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick > > > > Hi Dusan, > > > > > > On Jan 26, 2014, at 15:36 , Douglas Greve > <[email protected]> wrote: > > > > > > > > Hi Dusan, find out where matlab is and add it to your path. Eg, on > my mac matlab is here > > > > > > /Applications/MATLAB_R2011b.app/bin/matlab > > > > > > In my .cshrc file, I have > > > set path = ($path /Applications/MATLAB_R2011b.app/bin/matlab) > > > > Should you use bash, add the following two lines to your .bashrc: > > > > PATH= /Applications/MATLAB_R2011b.app/bin/matlab:$PATH > > export PATH > > > > Or you can put a symbolic link to the matlab binary to a directory > that is already in your path: > > "ln -s /Applications/MATLAB_R2011a.app/bin/matlab /usr/local/bin/matlab" > > (the first is more comprehensive and will also allow mex from the > terminal, but I do not think that you really care for that too much...) > > > > > > > > (In case you wonder what shell you use, type "echo $0" in a terminal: > > hms-beagle:~ moeller$ echo $0 > > -bash > > hms-beagle:~ moeller$ tcsh > > [hms-beagle:~] moeller% echo $0 > > tcsh > > [hms-beagle:~] moeller% > > > > e.g. I run bash by default, but after starting tcsh it reports tcsh; > for bash edit ~/.bashrc, for tcsh edit ~/.cshrc. I think that the nano > editor is part of macosx, so "nano ~/.bashrc" or "nano ~/.cshrc" > should work, edit the file then use control-x to exit nano, it will > ask whether you want to save…) > > > > best > > Sebastian > > > > > > > > doug > > > > > > > > > > > > On 1/26/14 9:28 AM, Dusan Hirjak wrote: > > >> Hi Sebastian, > > >> > > >> I typed "matlab" and "getmatlab" in my terminal, but it did not > work. When I typed getmatlab in my terminal I got the following > message: "ERROR: Cannot find matlab. Does not exist or is not in path." > > >> > > >> Typing "matlab" is not working either:-( "command not found" is > the answer. > > >> > > >> I guess your hypothesis is true and the matlab binary is not in > my path. Why not? What should I do next? > > >> > > >> Thanks a lot! > > >> > > >> DH > > >> > > >> > > >> > Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick > > >> > From: [email protected] > > >> > Date: Sun, 26 Jan 2014 10:33:33 +0100 > > >> > CC: [email protected] > > >> > To: [email protected] > > >> > > > >> > Hi Dusan, > > >> > > > >> > (I saw your PN earlier but had no idea and hence did not reply). > > >> > But this has more information, so I try again ;) > > >> > > > >> > > > >> > On Jan 25, 2014, at 02:00 , Dusan Hirjak > <[email protected]> wrote: > > >> > > > >> > > Dear Freesurferexperts, > > >> > > > > >> > > I still have the Problem because I can not run the the > mris-command to estimate the gyrification-index, because Freesurfer is > not recognizing Matlab: "ERROR: Matlab is required to run > mris_compute_lgi" > > >> > > Im not sure why this is happening? Does someone have an idea??? > > >> > > > >> > Could you, please open a terminal and type: 'matlab'. It should > open a matlab window, but I suspect that it does not work on your > system. My hypothesis is that either the binary/script to start matlab > is not called matlab (unlikely) or that the directory with the matlab > binary is not in your path and hence LGI can not start matlab. > > >> > Anyway, if calling "matlab" from the terminal works my > hypothesis is falsified, but give it a try, please. > > >> > > > >> > best regards > > >> > Sebastian > > >> > > > >> > > > >> > > > >> > > > > >> > > Im starting Freesurfer as follows: > > >> > > > > >> > > FREESURFER_HOME=/Users/dhirjak/freesurfer > > >> > > > > >> > > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > >> > > > > >> > > (than I get the following output) > > >> > > > > >> > > Dusan-Hirjaks-MacBook-Pro:~ dhirjak$ source > $FREESURFER_HOME/SetUpFreeSurfer.sh > > >> > > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 > -------- > > >> > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > >> > > FREESURFER_HOME /Users/dhirjak/freesurfer > > >> > > FSFAST_HOME /Users/dhirjak/freesurfer/fsfast > > >> > > FSF_OUTPUT_FORMAT nii.gz > > >> > > SUBJECTS_DIR /Users/dhirjak/MRI/Freesurfer_2 > > >> > > MNI_DIR /Users/dhirjak/freesurfer/mni > > >> > > FSL_DIR /Users/dhirjak/fsl > > >> > > > > >> > > export SUBJECTS_DIR=/Users/dhirjak/MRI/Freesurfer > > >> > > > > >> > > > > >> > > In have the following lines in my matlab startup-file: > > >> > > > > >> > > fshome = getenv('FREESURFER_HOME'); > > >> > > fsmatlab = sprintf('%s/matlab',fshome); > > >> > > if (exist(fsmatlab) == 7) > > >> > > path(path,fsmatlab); > > >> > > end > > >> > > clear fshome fsmatlab; > > >> > > fsfasthome = getenv('FSFAST_HOME'); > > >> > > fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); > > >> > > if (exist(fsfasttoolbox) == 7) > > >> > > path(path,fsfasttoolbox); > > >> > > end > > >> > > clear fsfasthome fsfasttoolbox; > > >> > > > > >> > > Thanks!!! > > >> > > > > >> > > Dusan Hirjak > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > _______________________________________________ > > >> > > Freesurfer mailing list > > >> > > [email protected] > > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > > > >> > > > > >> > > 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 . 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. > > >> > > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> > > >> [email protected] > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > [email protected] > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > 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 . 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. > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
