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.
