New subject: [External] question about mri_segment_hypothalamic_subunits {Disarmed}

8 Oct 2020


      External Email - Use Caution
Hello Victor,
If you used the 7.1.1 installer package,&nbsp;https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-darw..., then it should have installed /Applications/freesurfer/7..1.1 for you. &nbsp;I believe the same is true for the 7.1.0 installer, i.e., /Applications/freesurfer/7.1.0, and similarly for the 7.0.0 installer. &nbsp;We set it up that way so the distributions would be separate. &nbsp;This allows people to switch among/compare the distributions by setting FRESURFER_HOME differently, e.g.,&nbsp;
$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1or$ export FREESURFER_HOME=/Applications/freesurfer/7.1.0etc….. then source’ing the shell setup script for either sh or csh, e.g., for sh$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
The installer packages create an uninstall script under each distribution, e.g., &nbsp;/Applications/freesurfer/{7.1.1, 7..1.0, 7.0.0}/uninstall.sh. &nbsp;So if you wanted to start with a clean install you could try running the uninstaller script(s), and then re-install using the .pkg files, e.g., &nbsp;to run the 7.1.1 installer,
$ sudo /Applications/freesurfer/7.1.1/uninstall.sh&nbsp;
- R.
On Oct 8, 2020, at 18:13, Iglesias Gonzalez, Juan E. &lt;JIGLESIASGONZALEZ@mgh.harvard.edu&gt; wrote:Hi Victor,I highly recommend that you keep both installations separate.Cheers,/Eugenio&nbsp;&nbsp;Juan Eugenio IglesiasSenior research fellowCMIC (UCL), MGH (HMS) and CSAIL (MIT)http://www.jeiglesias.com%C2%A0%C2%A0%C2%A0%C2%A0From:%C2%A0%3Cfreesurfer-bo...; on behalf of "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" &lt;vzeng@bidmc.harvard.edu&gt;Reply-To:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;Date:&nbsp;Thursday, October 8, 2020 at 17:54To:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;[Freesurfer] question about mri_segment_hypothalamic_subunits&nbsp;Hi all,&nbsp;&nbsp;I installed the most recent dev version of FS7.1, and copied its files over the old FS7.1. I entered sudo mri_segment_hypothalamic_subunits into xquartz, and receive an error:&nbsp;&nbsp;error: freesurfer has not properly been sourced&nbsp;I am using mac os Catalina 10.15.6. How can I fix this?&nbsp;Victor ZengBeth Israel Deaconess Medical CenterKeshavan Lab--&nbsp;This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer%E2%80%8B