No worries, it happens to all of us 😊 Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Rosalia Dacosta Aguayo Sent: Monday, June 21, 2021 11:07 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem to run recon-all in one subject

External Email - Use Caution Hi Bruce,

Yes, I noticed that I did not include the extension by error.

Sorry for this childish error.

Kind regards, Rosie

On Mon, Jun 21, 2021 at 5:06 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Rosalia

Does /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w exist? Shouldn’t it have an extension like .nii.gz or .mgz? Cheers Bruce

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 Rosalia Dacosta Aguayo Sent: Monday, June 21, 2021 10:49 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Problem to run recon-all in one subject

External Email - Use Caution Dear Freesurfer's experts

I am trying to run recon-all -all in a subject and it seems there is a problem I do not know how to solve.

rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -s sub-001_ses-BSL -i /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w -T2 /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w -T2pial -all ERROR: cannot find /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu SMP Thu Nov 9 15:37:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-001_ses-BSL exited with ERRORS at Mon 21 Jun 16:45:13 CEST 2021

For more details, see the log file (there is no log file created) 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/BugReportinghttp://secure-web.cisco.com/1fl8R1eHZCuzU6FCHJEl-s4FAaPFJk5v8HULKxGhhH_IJIsARqvi_8ax2RUjFc8s-_n3e2QIM4j_u3OblOnyKy_FBZpW6j9ACXnftYLjq-Q8-yFdoaQEzTa_XWjvxO_GR0SlhaxNDLUcEwfR9Nh1DQ1dv5eKkTlJqZc8WYOQLxTRIF181QNN89uOty1MTFJ-viI9cFystqaf-GJkIgGiOnggNNi5JXT4BhS9hLC0fUV_xcu2HBdFAcQkXuy3xw5z5XMik90hv2FYMY8SaNgnpqg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ cd ARTICO rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/ARTICO $ ls fsaverage sub-001_ses-BSL_T2w.nii sub-003_ses-BSL_T1w.nii sub-001_ses-BSL_T1w.nii sub-003_ses-BSL sub-003_ses-BSL_T2w.nii rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/ARTICO $

Any idea would be very appreciated.

Kind regards, Rosie

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