Hello FS'users,
I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but the problem is that I have Installed matlab in a computer (windows) and FS in another one (ubuntu) Can I configure something to use the FS commands in matlab in order to obtain some graphs? And also, where can I find the cortical thickness in each regions (Brodmann areas, gyrus or sulci) of the brain in order to compare a normal patient with a patiwnt who has a cortical dysplasia ?
Thanks a lot for your help,
Carolina
Hi Carolina There is a directory freesurfer/matlab which contains several matlab-based scripts for reading and writing (after modified) surface- and volume-based data generated in freesurfer. Transport files from Linux to Windows will be tedious and things may not work properly, therefore, I recommend you to install Matlab for Linux or you can try with Octave (a kind of GNU Matlab for Linux). Cheers Jorge
--- El mar, 5/7/11, Carolina Valencia cvalencia@linkdx.com.co escribió:
De: Carolina Valencia cvalencia@linkdx.com.co Asunto: [Freesurfer] Matlab and FS Para: freesurfer@nmr.mgh.harvard.edu Fecha: martes, 5 de julio, 2011 17:39
Hello FS'users,
I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but the problem is that I have Installed matlab in a computer (windows) and FS in another one (ubuntu) Can I configure something to use the FS commands in matlab in order to obtain some graphs? And also, where can I find the cortical thickness in each regions (Brodmann areas, gyrus or sulci) of the brain in order to compare a normal patient with a patiwnt who has a cortical dysplasia ?
Thanks a lot for your help,
Carolina
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Hi Jorge, Thanks for your reply, I installed Octave in the Ubuntu machine, Should I setup something in order to use the FS commands? Best regards, Carolina
2011/7/5 jorge luis jbernal0019@yahoo.es
Hi Carolina
There is a directory freesurfer/matlab which contains several matlab-based scripts for reading and writing (after modified) surface- and volume-based data generated in freesurfer. ****
Transport files from Linux to Windows will be tedious and things may not work properly, therefore, I recommend you to install Matlab for Linux or you can try with Octave (a kind of GNU Matlab for Linux).****
Cheers ****
Jorge****
--- El *mar, 5/7/11, Carolina Valencia cvalencia@linkdx.com.co*escribió:
De: Carolina Valencia cvalencia@linkdx.com.co Asunto: [Freesurfer] Matlab and FS Para: freesurfer@nmr.mgh.harvard.edu Fecha: martes, 5 de julio, 2011 17:39
Hello FS'users,
I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but the problem is that I have Installed matlab in a computer (windows) and FS in another one (ubuntu) Can I configure something to use the FS commands in matlab in order to obtain some graphs? And also, where can I find the cortical thickness in each regions (Brodmann areas, gyrus or sulci) of the brain in order to compare a normal patient with a patiwnt who has a cortical dysplasia ?
Thanks a lot for your help,
Carolina
-----Adjunto en línea a continuación-----
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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 Carolina You simply need to add the path ‘your FS installation dir/freesurfer/matlab’ to the search path in Octave: addpath(‘your FS installation dir/freesurfer/matlab’); For example, to build a histogram of cortical thickness values for the first subject of your study, you can try: thickness_data = squeeze(load_mgh(‘lh.thickness.mgh’)); hist(thickness_data(:,1)); where lh.thickness.mgh contains the thickness data for the left hemisphere of your subjects (eg.. those generated with mris_preproc) Cheers Jorge
--- El jue, 7/7/11, Carolina Valencia cvalencia@linkdx.com.co escribió:
De: Carolina Valencia cvalencia@linkdx.com.co Asunto: Re: [Freesurfer] Matlab and FS Para: "jorge luis" jbernal0019@yahoo.es CC: freesurfer@nmr.mgh.harvard.edu Fecha: jueves, 7 de julio, 2011 15:30
Hi Jorge, Thanks for your reply, I installed Octave in the Ubuntu machine, Should I setup something in order to use the FS commands? Best regards, Carolina
2011/7/5 jorge luis jbernal0019@yahoo.es
Hi Carolina There is a directory freesurfer/matlab which contains several matlab-based scripts for reading and writing (after modified) surface- and volume-based data generated in freesurfer. Transport files from Linux to Windows will be tedious and things may not work properly, therefore, I recommend you to install Matlab for Linux or you can try with Octave (a kind of GNU Matlab for Linux). Cheers Jorge
--- El mar, 5/7/11, Carolina Valencia cvalencia@linkdx.com.co escribió:
De: Carolina Valencia cvalencia@linkdx.com.co Asunto: [Freesurfer] Matlab and FS Para: freesurfer@nmr.mgh.harvard.edu Fecha: martes, 5 de julio, 2011 17:39
Hello FS'users,
I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but the problem is that I have Installed matlab in a computer (windows) and FS in another one (ubuntu) Can I configure something to use the FS commands in matlab in order to obtain some graphs? And also, where can I find the cortical thickness in each regions (Brodmann areas, gyrus or sulci) of the brain in order to compare a normal patient with a patiwnt who has a cortical dysplasia ?
Thanks a lot for your help,
Carolina
-----Adjunto en línea a continuación-----
_______________________________________________ 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 Carolina,
the thickness in each region can be obtained either from the aparc.stats file or in matlab by loading the thickness using read_curv.m and the various label files with read_label.m. Make sure to account for the indices being one-based in the return from read_curv.m, but zero-based in the label.
cheers Bruce
On Tue, 5 Jul 2011, Carolina Valencia wrote:
Hello FS'users,
I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but the problem is that I have Installed matlab in a computer (windows) and FS in another one (ubuntu) Can I configure something to use the FS commands in matlab in order to obtain some graphs? And also, where can I find the cortical thickness in each regions (Brodmann areas, gyrus or sulci) of the brain in order to compare a normal patient with a patiwnt who has a cortical dysplasia ?
Thanks a lot for your help,
Carolina
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Carolina Valencia -
jorge luis