External Email - Use Caution
The message suggested subdirectory 'test1' already exists in your $SUBJECTS_DIR.
Pass a different subjid to -s <>, or delete directory 'test1'.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Pedro henrique barradas
Sent: Friday, May 12, 2023 4:00 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cannot find subject for recon-all
External Email - Use Caution
Thank you very much! It seemed to work but now it gives me another error message
Pedros-Air:test1 pedrobarradas$ recon-all -i $SUBJECTS_DIR/test1/01.nii -s
$SUBJECTS_DIR/test1 -all
ERROR: You are trying to re-run an existing subject with (possibly)
new input data (-i). If this is truly new input data, you should delete
the subject folder and re-run, or specify a different subject name.
If you are just continuing an analysis of an existing subject, then
omit all -i flags.
________________________________
De:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
em nome de Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Enviado: segunda-feira, 1 de maio de 2023 18:20
Para: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Assunto: Re: [Freesurfer] Cannot find subject for recon-all
External Email - Use Caution
Hi Pedro,
You need to provide full path to your .nii files.
You also need to set environment variable SUBJECTS_DIR to the directory you
have write permission.
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Pedro henrique barradas
Sent: Monday, May 1, 2023 12:06 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Cannot find subject for recon-all
External Email - Use Caution
Hello!
I have recently installed freesurfer and was attempting to reconstruc some
exams but I keep getting this error message
Pedros-Air:subjects pedrobarradas$ recon-all -i 01.nii. -s test1 -all
ERROR: cannot find 01.nii.
recon-all -s exited with ERRORS at Mon May 1 16:51:37 WEST 2023
For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://secure-web.cisco.com/1hYYBNnE0zViHLTfpy8vlUPODh2mEWusrsXcrii0Ua57OWj3rej3i7KKrQ_9MBI1ajI7gPXk5KFgiEBQ5Ka0NiOUGTSmL-ZkqM-4pDL48fg10CUQdoHNtNED0tw6sLAerbTcCJ8GrCNnqVcZ0gdJIxWAYxtqWIdXjlHOmj0jck5RlEIJksxEnXrwJ65FYqVhHPoU8qYz-J4cQzVLsUwieiD979nEESfA7RhJfnwEovXveCT9RXEUFCT_QXy7JTSSVkyuvX6QLDRv2qw0M8qOXMg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting<http://secure-web.cisco.com/1RNbgC5ak4nQL1JrC4tKj3GSvCQkHEsU7ie26A1Ir2qdWeoy-ESTvP5BicYKj__hQxtR3Xdrdcr3mRfLEziNuf8dAs0lf1xJ4b25ZavProw6FvSJISdbP0nyLkd9jXZV7uX85kV8QY-hQM7GJKpQF4B3KFkPzvjBWbMP4zWTyJv671kJJ0_hY43Hy639F6XwBNCsDIgi9KNzqHZTqxagMijobVijhjYFLErJTeBV7Ee0LdkPflhCK7_sfciKm3Oxqr31hFsFB4PymgGO9yn-oYw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>
I'm not sure what I am doing wrong.
Any help would be tremendousy appreciated.
Best Wishes
Pedro Barradas
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