We downloaded the tar.gz version of the mac FS dev. I'll try and download the .pkg. Perhaps it doesnt work as a tar.gz
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: fsbuild fsbuild@contbay.com Sent: Thursday, October 8, 2020 7:29 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Zeng,Victor (BIDMC - Keshavan - Psychiatry) Subject: [External] [Freesurfer] question about mri_segment_hypothalamic_subunits
Hello Victor,
If you used the 7.1.1 installer package, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-darw...https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_pub_dist_freesurfer_7.1.1_freesurfer-2Ddarwin-2DmacOS-2D7.1.1.pkg&d=DwMFaQ&c=WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=ziAm16qmlGqGtX5PhV9Harh0DYcHWCNZ9xWh5fPQIi0&m=J55-PbeR_bO2H-H0-DkhFFLsih-JjSq7rSLnmEZolLQ&s=nItI5RDITVIqjlsRun6gpef7JvMsi_FHjXxfrnrXYEk&e=, then it should have installed /Applications/freesurfer/7.1.1 for you. 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. We set it up that way so the distributions would be separate. This allows people to switch among/compare the distributions by setting FRESURFER_HOME differently, e.g.,
$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1 or $ export FREESURFER_HOME=/Applications/freesurfer/7.1.0 etc... .. 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., /Applications/freesurfer/{7.1.1, 7.1.0, 7.0.0}/uninstall.sh. 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., to run the 7..1.1 installer,
$ sudo /Applications/freesurfer/7.1.1/uninstall.sh
- R.
On Oct 8, 2020, at 18:13, Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu wrote:
Hi Victor, I highly recommend that you keep both installations separate. Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.comhttps://urldefense.proofpoint.com/v2/url?u=http-3A__www.jeiglesias.com_&d=DwMFaQ&c=WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=ziAm16qmlGqGtX5PhV9Harh0DYcHWCNZ9xWh5fPQIi0&m=J55-PbeR_bO2H-H0-DkhFFLsih-JjSq7rSLnmEZolLQ&s=LtYyzwiN92nVgG8YttteSSdjNq74ngVOjoImXhVVB2Y&e=
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" <vzeng@bidmc.harvard.edumailto:vzeng@bidmc.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, October 8, 2020 at 17:54 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] question about mri_segment_hypothalamic_subunits
?Hi all,
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:
error: freesurfer has not properly been sourced
I am using mac os Catalina 10.15.6. How can I fix this? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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