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 <fis...@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 <fis...@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 >> <zkauf...@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" >> <zkauf...@nmr.mgh.harvard.edu >> > <mailto:zkauf...@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" >> > <fis...@nmr.mgh.harvard.edu >> <mailto:fis...@nmr.mgh.harvard.edu> >> > > <mailto:fis...@nmr.mgh.harvard.edu >> > <mailto:fis...@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. >> >> >> >> > _______________________________________________ > 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 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.
