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 The recon-all log contains this entry,

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

If you go to where that log file is, which I think would be,

$ cd $SUBJECTS_DIR/mri/transforms

… then look in that log file to see what the error is.  It is usually at the end of the log file.

- R.


On Feb 9, 2024, at 07:16, Francesco Lomi <francesco.lomi@unifi.it> wrote:

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Unfortunately I've tried to change the directory but I've encountered the same error, as shown in the log file. 
Best,
Francesco

Il giorno gio 8 feb 2024 alle ore 17:59 Huang, Yujing <YHUANG43@mgh.harvard.edu> ha scritto:

This is from your recon-all.log: 

“

setenv SUBJECTS_DIR /home/ubuntu/freesurfer/subjects

FREESURFER_HOME /home/ubuntu/freesurfer

Actual FREESURFER_HOME /home/ubuntu/Freesurfer

“

Your SUBJECTS_DIR points to your Freesurfer install directory - /home/ubuntu/freesurfer/subjects. I’m not sure if this is the reason for the failure. But it is a good idea to set SUBJECTS_DIR to some other directory where you have write permissions.

 

Can you re-set SUBJECTS_DIR and try again?

 

Best,

 

Yujing

 

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Francesco Lomi
Sent: Thursday, February 8, 2024 11:44 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mpr2mni305 failed

 

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Yes, sure. This is the file

Thanks. 

 

Il giorno gio 8 feb 2024 alle ore 17:03 Huang, Yujing <YHUANG43@mgh.harvard.edu> ha scritto:

Can you re-send recon-all.log as attachment?

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Francesco Lomi
Sent: Thursday, February 8, 2024 10:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mpr2mni305 failed

 

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Hello everybody,

 

I'm new on Freesurfer and I've installed the software on my Ubuntu 20.04 machine. The installation should be fine. just tried to run recon-all on my subject data but i got stuck on the following error you can see on the screenshot:

 

<image001.png>

 

Any idea on how to fix this?

Thank you in advance

 

Best,

Francesco

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