18 Nov
2014
18 Nov
'14
9:16 a.m.
Hi Gunjan
if you are using bash, you need to run the instructions for bash at:
http://freesurfer.net/fswiki/SetupConfiguration
for example, it says:
If using bash or sh, type:
export FREESURFER_HOME=<freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
cheers Bruce
On Tue, 18 Nov 2014, Gunjan Gautam wrote:
I followed the installation process from http://freesurfer.net/fswiki/LinuxInstall.
while running "setenv FREESURFER_HOME /usr/local/freesurfer" it shows that setenv command not found.
Is it necessary to place FreeSurfer directory in to /usr/local ? I have it on my desktop.
On Tue, Nov 18, 2014 at 6:47 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: I think if the file existed you would have gotten a syntax error. Does it exist? If not, then either you didn't install FreeSurfer there or something went wrong with your installation
cheers Bruce On Tue, 18 Nov 2014, Gunjan Gautam wrote: I ran but its showing error like below: bibl04@BIBL04:~/Desktop/freesurfer$ source /Desktop/freesurfer/SetUpFreeSurfer.csh bash: /Desktop/freesurfer/SetUpFreeSurfer.csh: No such file or directory May be due to the shell. What should I do now? On Tue, Nov 18, 2014 at 6:37 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Gunjan FREESURFER_HOME should be an environment variable, not the name of a directory. It should point to the directory that you installed FreeSurfer in. You should run: source <installation directory>/SetUpFreeSurfer.csh before trying to run anything cheers Bruce On Tue, 18 Nov 2014, Gunjan Gautam wrote: Hello Sir, I have place the "license.txt" in the same directory that contains build-stamp.txt as there were no directory with name "FREESURFER_HOME". freeview command is not working and showing below message "freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory". What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: > Sir earlier I was trying to use FreeSurfer using Virtual Box in my > Windows machine. There the mri_convert command did not work so I > switched to a Linux machine. Now, I'm using centos6_x86_64 version as my > machine has the Ubuntu 12.04 platform and here also facing the same > problem. > > I want to share one thing that in my institute I tried hard to download > FreeSurfer but every time it resulted into a time-out situation so I had > to ask someone to get it downloaded and send me through Google drive. > This was how I installed it in my system. > > Best regards, > Gunjan > > On Nov 12, 2014 9:15 PM, "Z K" <zkaufman@nmr.mgh.harvard.edu > <mailto:zkaufman@nmr.mgh.harvard.edu>> wrote: > > Gunjan, > > Are you using your own version of VirtualBox, with freesurfer installed > on it by you? Or the VirtualBox version of freesurfer made by us and > downloaded from our website? I am confused because in your email below, > freesurfer appears to be installed on the Desktop whereas the > prepackaged version made by us is installed in /usr/local > > -Zeke > > On 11/12/2014 08:54 AM, Gunjan Gautam wrote: > > Hello Sir, > > > > License file is present in the folder but with the name LICENSE. > Should > > I download it again ? > > > > Best Regards, > > Gunjan > > > > On Nov 12, 2014 7:01 PM, "Bruce Fischl" > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > > > Hi Gunjan > > > > do you have a license? If not you need to download and install it > > (as noted in the error message). They are free. > > > > cheers > > Bruce > > On Wed, 12 Nov 2014, Gunjan Gautam wrote: > > > > > > Hello Sir, > > > > I'm using FreeSurfer through Virtual Box. I tried the below > > command for > > reslicing my volume according to a reference volume but the > > process gets > > stuck at " reading volume". > > > > mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz > > > > A: Volume to be resampled / resliced > > B: Reference Volume > > > > Error message is being shown like below: > > > > mri_convert a.nii a.resliced.nii -rl b.nii > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 > mreuter Exp $ > > reading from a.nii... > > > ------------------------------__------------------------------__-------- - - ---- > > ERROR: Invalid FreeSurfer license key found in license file > > /home/bibl04/Data_Home/__Desktop/freesurfer/license.txt > > If you are outside the NMR-Martinos Center, > > go to http://surfer.nmr.mgh.harvard.__edu > > <http://surfer.nmr.mgh.harvard.edu> to > > get a valid license file (it's free). > > If you are inside the NMR-Martinos Center, > > make sure to source the standard environment. > > > > Actually, I have two volumes, belong to the same subject. One > > volume is the > > ground truth which will be considered as standard for the > second > > volume > > which is the processed one or the extracted brain. To > perform a > > perfect > > comparison between both volumes, these must generate equal > > number of slices > > in order to compare the corresponding slide. But here > there is > > problem with > > my volumes, that is while performing slicing Ground Truth > volume is > > generating 360 slice and processed volume is generating 181 > > slides. So > > comparison can't take place in this way. > > > > What all I need is to do the resampling or generating the 181 > > slides from > > the Ground Truth as well. > > > > > > Best Regards, > > Gunjan > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 > _______________________________________________ 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.
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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.