External Email - Use Caution 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 (< fis...@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 < > miguelrivasf...@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* > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Miguel Ángel Rivas Fernández*
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