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Dear Yujing,

Thank you so much for your help.
It turned out the link was missing when we copied our subject data from the web server to the drive.
(I tried your command to create the link, but it did not work, making us realise something was wrong elsewhere.)

Many thanks!

Best,
Asuka



From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@MGH.HARVARD.EDU>
Sent: 07 February 2024 14:33
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] make_average_subject command error
 

If you run recon-all, ?h.pial will appear as symbolic links to ?h.pial.T1.  Here is the list of symbolic links you should find in your subject/surf directory:

 

rh.pial -> rh.pial.T1

lh.pial -> lh.pial.T1

rh.fsaverage.sphere.reg -> rh.sphere.reg

lh.fsaverage.sphere.reg -> lh.sphere.reg

rh.white.K -> rh.white.preaparc.K

rh.white.H -> rh.white.preaparc.H

lh.white.K -> lh.white.preaparc.K

lh.white.H -> lh.white.preaparc.H

 

I’m wondering why the symbolic links are not created.

 

To create the symbolic links,

1. cd to subject/surf directory

2. run ln command to create each link, for example, ‘ln -s lh.pial.T1 lh.pial’

 

Best,

 

Yujing

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Asuka Toyofuku
Sent: Wednesday, February 7, 2024 5:13 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] make_average_subject command error

 

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Dear Freesurfer experts,

 

We're trying to make an average subject for group analysis using Freesurfer 7.1, but the make_average_subject command exits with errors after calling make_average_surf:

 

MakeAverageSurf(): 129 lh pial sphere.reg talairach.xfm 1 1

 

It appears to be trying to find the lh.pial surface for the first participant, but this file is named "lh.pial.T1". (In FS 5.3 and 6.0, this file was labelled "lh.pial", but with FS7.1, it seems to be named lh.pial.T1).

 

Does anyone have a suggestion for how to fix this problem? (We want to avoid changing all the file names to "lh.pial" from "il.pial.T1")

Should we call make_average_subject again with -no-surf-to-surf ?

 

Best regards,

Asuka