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It worked! Thank you so much for fixing this.

I am also trying to open ?h.pial-outer-smoothed file. How should I proceed with either freeview or tksurferfv? Haven't found any info regarding this on the wiki!

Again, thank you so much for your help!

All the best

On Wed, Aug 18, 2021 at 11:37 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

This is fixed in v7.2, but if you want to patch your current freesurfer distribution, you can try these commands:

cd $FREESURFER_HOME/bin

sudo mv fsvglrun fsvglrun.backup

sudo curl -O https://secure-web.cisco.com/1efCCkX86LzSzP4WTrfKmXAn_UMOkClX1vXHyTzq468M8Eq...

sudo chmod +x fsvglrun

best

Andrew

*From: *freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < ladn@email.gwu.edu> *Date: *Tuesday, August 17, 2021 at 2:43 PM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] LGI - output issue

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Good afternoon FreeSurfer experts,

Hope that everyone is well and staying safe!

I tried opening LGI freeview (or tksurferfv) output, and I have been running into the following issues (see code and error message outputs below). Any ideas how I could fix this? Please let me know if additional details are needed.

Bolded code is what I inserted. Outputs are not bolded.

*tksurfer HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi*

zsh: command not found: tksurfer

*tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi*

ERROR: cannot find lh.pial_lgi

*cd $SUBJECTS_DIR/HAR30303_srs2_2/surf*

*tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi*

freeview -f /Applications/ace_complete/HAR30303_srs2_2/surf/lh.inflated:curvature=/Applications/ace_complete/HAR30303_srs2_2/surf/lh.curv:overlay=lh.pial_lgi:overlay_threshold=2,2,5 -viewport 3d

/Applications/freesurfer/bin/fsvglrun: line 20: conditional binary operator expected

/Applications/freesurfer/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN'

/Applications/freesurfer/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then'

Also within the surf folder, I tried something like: *freesurfer -v lh.pial_lgi*

Output in freeview was just a dark screen - tried changing the color map but nothing improved this issue.

Thank you so much!

---

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