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Hi Bruce,

What an absurd mistake, sorry.

However, I ran the command and I got the following error:

pcpb3846:~ lab1-rmn$ recon-all -autorecon2-cp -autorecon3 -subjid 5054
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
-rwxr-xrwx  1 root  wheel  508088 Sep 28 19:52 /Applications/freesurfer/subjects/5054/scripts/recon-all.log
Darwin pcpb3846.inv.usc.es 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64
#--------------------------------------------
#@# Intensity Normalization2 Fri Sep 28 23:13:36 CEST 2018
/Applications/freesurfer/subjects/5054/mri
\n mri_normalize -f /Applications/freesurfer/subjects/5054/tmp/control.dat -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz \n
mghRead(/Applications/freesurfer/subjects/5054/mri/aseg.presurf.mgz, -1): could not open file
using control points from file /Applications/freesurfer/subjects/5054/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.presurf.mgz
mri_normalize: could not read aseg from file aseg.presurf.mgz
Darwin pcpb3846.inv.usc.es 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64

recon-all -s 5054 exited with ERRORS at Fri Sep 28 23:13:38 CEST 2018

For more details, see the log file /Applications/freesurfer/subjects/5054/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Why?


Thanks for your help,

Best,

El vie., 28 sept. 2018 a las 19:38, Bruce Fischl (<fischl@nmr.mgh.harvard.edu>) escribió:
Looks like you have an incorrect space after the word recon 

On Sep 28, 2018, at 1:35 PM, Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com> wrote:

        External Email - Use Caution        


Hi Freesurfer devs, 


I tried to re run the recon -all after put some control points in the brainmask and I get the following error:


pcpb3846:~ lab1-rmn$ recon -all -autorecon2-cp -autorecon3 -4025 cp_before

-bash: recon: command not found




What could be the problem? The Freesurfer version that I am using at this moment is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c




Thanks in advance, 



Best, 
--
Miguel Ángel Rivas Fernández
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--
Miguel Ángel Rivas Fernández