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 mgrameshbabu2013@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 zkaufman@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.