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??? 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/freesurferFSFAST_HOME /Users/dhirjak/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /Users/dhirjak/MRI/Freesurfer_2MNI_DIR /Users/dhirjak/freesurfer/mniFSL_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
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 dusanhirjak@hotmail.com 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 Freesurfer@nmr.mgh.harvard.edu 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.
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: sebastian.moeller1@rwth-aachen.de Date: Sun, 26 Jan 2014 10:33:33 +0100 CC: freesurfer@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com
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 dusanhirjak@hotmail.com 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 $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Users/dhirjak/freesurfer FSFAST_HOME /Users/dhirjak/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/dhirjak/MRI/Freesurfer_2 MNI_DIR /Users/dhirjak/freesurfer/mni FSL_DIR /Users/dhirjak/fsl
export SUBJECTS_DIR=/Users/dhirjak/MRI/Freesurfer
In have the following lines in my matlab startup-file:
fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox;
Thanks!!!
Dusan Hirjak
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Dusan, find out where matlab is and add it to your path. Eg, on my mac matlab is here
/Applications/MATLAB_R2011b.app/bin/matlab
In my .cshrc file, I have set path = ($path /Applications/MATLAB_R2011b.app/bin/matlab)
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: sebastian.moeller1@rwth-aachen.de Date: Sun, 26 Jan 2014 10:33:33 +0100 CC: freesurfer@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com
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 dusanhirjak@hotmail.com
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
$FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Users/dhirjak/freesurfer FSFAST_HOME /Users/dhirjak/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/dhirjak/MRI/Freesurfer_2 MNI_DIR /Users/dhirjak/freesurfer/mni FSL_DIR /Users/dhirjak/fsl
export SUBJECTS_DIR=/Users/dhirjak/MRI/Freesurfer
In have the following lines in my matlab startup-file:
fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox;
Thanks!!!
Dusan Hirjak
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Dusan,
On Jan 26, 2014, at 15:36 , Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Dusan, find out where matlab is and add it to your path. Eg, on my mac matlab is here
/Applications/MATLAB_R2011b.app/bin/matlab
In my .cshrc file, I have set path = ($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: sebastian.moeller1@rwth-aachen.de Date: Sun, 26 Jan 2014 10:33:33 +0100 CC: freesurfer@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com
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 dusanhirjak@hotmail.com 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 Freesurfer@nmr.mgh.harvard.edu 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
Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
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: sebastian.moeller1@rwth-aachen.de Date: Sun, 26 Jan 2014 16:33:40 +0100 To: greve@nmr.mgh.harvard.edu CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
Hi Dusan,
On Jan 26, 2014, at 15:36 , Douglas Greve greve@nmr.mgh.harvard.edu 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: sebastian.moeller1@rwth-aachen.de Date: Sun, 26 Jan 2014 10:33:33 +0100 CC: freesurfer@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com
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 dusanhirjak@hotmail.com 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 Freesurfer@nmr.mgh.harvard.edu 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
Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: sebastian.moeller1@rwth-aachen.de Date: Sun, 26 Jan 2014 16:33:40 +0100 To: greve@nmr.mgh.harvard.edu CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
Hi Dusan,
On Jan 26, 2014, at 15:36 , Douglas Greve
greve@nmr.mgh.harvard.edu 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: sebastian.moeller1@rwth-aachen.de Date: Sun, 26 Jan 2014 10:33:33 +0100 CC: freesurfer@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com
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
dusanhirjak@hotmail.com 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
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Douglas Greve -
Douglas N Greve
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Dusan Hirjak -
Sebastian Moeller