External Email - Use Caution
Dear FreeSurfer community,
I am running a retinotopy analysis using FSFAST and I encountered a problem with data visualisation. To perform my analysis I followed the official guidelines found here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis and the following tutorial: https://kylemathewson.com/retinotopy-in-freesurfercnl-protocol/#FUNC
The pipeline worked and I didn't get any error messages.
I now want to visualise my single subject data to make sure that everything worked fine. As suggested here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis I run a command: tksurfer-sess -s 2016_09_23_NBI_AMJU -hemi lh -analysis retino.self.lh
Unfortunately, it doesn't work and returns the following error message: /Applications/freesurfer/7.1.0/bin/fsvglrun: line 20: conditional binary operator expected /Applications/freesurfer/7.1.0/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/freesurfer/7.1.0/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then'
I attached in this mail a print screen with the logs of the operation. I believe that the program is supposed to create a file: retino.self.lh/tksconcat.nii but I don't find it in my analysis folder.
Could anyone help me resolve this issue? Thank you! Kasia
[image: image.png]
That is kind of strange. What happens if you run
fsvglrun ls
On 5/15/2020 5:30 AM, Kasia Siuda-Krzywicka wrote:
External Email - Use Caution
Dear FreeSurfer community,
I am running a retinotopy analysis using FSFAST and I encountered a problem with data visualisation. To perform my analysis I followed the official guidelines found here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis and the following tutorial: https://kylemathewson.com/retinotopy-in-freesurfercnl-protocol/#FUNC
The pipeline worked and I didn't get any error messages.
I now want to visualise my single subject data to make sure that everything worked fine. As suggested here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis I run a command: tksurfer-sess -s 2016_09_23_NBI_AMJU -hemi lh -analysis retino.self.lh
Unfortunately, it doesn't work and returns the following error message: /Applications/freesurfer/7.1.0/bin/fsvglrun: line 20: conditional binary operator expected /Applications/freesurfer/7.1.0/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/freesurfer/7.1.0/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then'
I attached in this mail a print screen with the logs of the operation. I believe that the program is supposed to create a file: retino.self.lh/tksconcat.nii but I don't find it in my analysis folder.
Could anyone help me resolve this issue? Thank you! Kasia
image.png
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Kasia Siuda-Krzywicka