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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> em nome de Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Enviado: segunda-feira, 1 de maio de 2023 18:20 Para: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Pedro henrique barradas Sent: Monday, May 1, 2023 12:06 PM To: freesurfer@nmr.mgh.harvard.edumailto: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/1hYYBNnE0zViHLTfpy8vlUPODh2mEWusrsXcrii0Ua57OWj3...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