Dear Z K, I have downloaded again by using the following command on the terminal;
wget http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz Then md5sum check; md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz d49e9dd61d6467f65b9582bddec653a4 freesurfer-Linux-centos6_x86_ 64-stable-pub-v6.0.0.tar.gz pc@RB:/usr/local$ ls freesurfer/ ASegStatsLUT.txt FreeSurferEnv.sh SetUpFreeSurfer.csh AUTHORS fsafd SetUpFreeSurfer.sh average fsfast Simple_surface_labels2009.txt bin lib sources.csh build-stamp.txt LICENSE sources.sh data matlab subjects DefectLUT.txt mni tkmeditParcColorsCMA diffusion NOTICE tktools docs README trctrain FreeSurferColorLUT.txt SegmentNoLUT.txt VERSION FreeSurferEnv.csh sessions WMParcStatsLUT.txt All the files have been downloaded. Working fine. Whenever I open my terminal it opens with the following message all the time. How to avoid it? bash: /usr/local/freesurfer/SetUpFreeSurfer.csh: line 43: syntax error: unexpected end of file -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 pc@RB:~$ Thanks RB On Sat, Apr 22, 2017 at 9:50 AM, Ramesh Babu <mgrameshbabu2...@gmail.com> wrote: > Dear ZK, > > I have done md5sum check. I got the following message. How to confirm it > is complete or not? > > pc@RB:~/Downloads$ md5sum > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz > > 5362fc776145b06ded219f42af4a8207 freesurfer-Linux-centos6_x86_ > 64-stable-pub-v6.0.0.tar.gz > > > Thanks > RB > > On Thu, Apr 20, 2017 at 7:32 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote: > >> I just did a test by downloading and extracting the tar, and I got all >> the expected files: >> >> /usr/local/fstemp/freesurfer/tkmeditParcColorsCMA >> /usr/local/fstemp/freesurfer/mni >> /usr/local/fstemp/freesurfer/sources.csh >> /usr/local/fstemp/freesurfer/docs >> /usr/local/fstemp/freesurfer/Simple_surface_labels2009.txt >> /usr/local/fstemp/freesurfer/NOTICE >> /usr/local/fstemp/freesurfer/FreeSurferColorLUT.txt >> /usr/local/fstemp/freesurfer/DefectLUT.txt >> /usr/local/fstemp/freesurfer/subjects >> /usr/local/fstemp/freesurfer/LICENSE >> /usr/local/fstemp/freesurfer/fsafd >> /usr/local/fstemp/freesurfer/ASegStatsLUT.txt >> /usr/local/fstemp/freesurfer/diffusion >> /usr/local/fstemp/freesurfer/average >> /usr/local/fstemp/freesurfer/bin >> /usr/local/fstemp/freesurfer/SetUpFreeSurfer.sh >> /usr/local/fstemp/freesurfer/SegmentNoLUT.txt >> /usr/local/fstemp/freesurfer/README >> /usr/local/fstemp/freesurfer/sources.sh >> /usr/local/fstemp/freesurfer/data >> /usr/local/fstemp/freesurfer/SetUpFreeSurfer.csh >> /usr/local/fstemp/freesurfer/tktools >> /usr/local/fstemp/freesurfer/FreeSurferEnv.sh >> /usr/local/fstemp/freesurfer/fsfast >> /usr/local/fstemp/freesurfer/WMParcStatsLUT.txt >> /usr/local/fstemp/freesurfer/VERSION >> /usr/local/fstemp/freesurfer/build-stamp.txt >> /usr/local/fstemp/freesurfer/trctrain >> /usr/local/fstemp/freesurfer/lib >> /usr/local/fstemp/freesurfer/FreeSurferEnv.csh >> /usr/local/fstemp/freesurfer/AUTHORS >> /usr/local/fstemp/freesurfer/matlab >> /usr/local/fstemp/freesurfer/sessions >> >> >> Perhaps your file was not yet complete, or it was corrupted in some way. >> The md5sum of the tarball is 'd49e9dd61d6467f65b9582bddec653a4' which >> you can get by typing: >> >> md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz >> >> >> On 04/20/2017 08:04 AM, Ramesh Babu wrote: >> > Dear Experts, >> > >> > I have installed in /usr/local/freesurfer. I am trying to follow the >> > command given in the freesurfer web page. >> > >> > $> export FREESURFER_HOME=/usr/local/freesurfer $> source >> > $FREESURFER_HOME/SetUpFreeSurfer.sh >> > >> > But I could not figure out the .sh file in the freesurfer folder. Please >> > see the list of files in the freesurfer folder given below. >> > >> > List of files in the freesurfer folder; >> > >> > /usr/local/freesurfer/average >> > /usr/local/freesurfer/fsafd >> > /usr/local/freesurfer/fsfast >> > /usr/local/freesurfer/lib >> > /usr/local/freesurfer/sessions >> > /usr/local/freesurfer/tktools >> > /usr/local/freesurfer/trctrain >> > /usr/local/freesurfer/DefectLUT.txt >> > /usr/local/freesurfer/FreeSurferColorLUT.txt >> > /usr/local/freesurfer/FreeSurferEnv.csh >> > /usr/local/freesurfer/LICENSE >> > /usr/local/freesurfer/SetUpFreeSurfer.csh >> > /usr/local/freesurfer/sources.csh >> > /usr/local/freesurfer/sources.sh >> > /usr/local/freesurfer/tkmeditParcColorsCMA >> > /usr/local/freesurfer/VERSION >> > /usr/local/freesurfer/WMParcStatsLUT.txt >> > >> > You can notice that there is no SetUpFreeSurfer.sh file. >> > >> > Details about my pc; >> > >> > >> > Ubuntu 16.04 LTS, 64 bit is installed. Running w8.1 via virtual box. >> > Freesurfer is installed in Ubuntu OS. >> > >> > >> > I am using bash shell. >> > >> > pc@RB:~$ echo $0 >> > bash >> > >> > pc@RB:~$ echo $SHELL >> > /bin/bash >> > >> > pc@RB:~$ ps -p "$$" >> > PID TTY TIME CMD >> > 3706 pts/1 00:00:00 bash >> > >> > Need your help to run freesurfer in my pc. >> > >> > >> > Thanks in advance >> > >> > Ramesh >> > >> > >> > >> > _______________________________________________ >> > 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.
