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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> em nome de Huang, Yujing <YHUANG43@mgh.harvard.edu>
Enviado: segunda-feira, 1 de maio de 2023 18:20
Para: Freesurfer support list <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.edu <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.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://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

 

 

I'm not sure what I am doing wrong.

Any help would be tremendousy appreciated.

 

Best Wishes

Pedro Barradas