Hi Salah - It looks like it didn't find your subject's freesurfer recon when it was doing the pre-processing, so it skipped some steps that you need to go beyond that point. Based on your SUBJECTS_DIR and your subject name, it looked for this file: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/mri/brain.mgz
Any chance this was missing or unreadable?
a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salah Showiheen sshowiheen@gmail.com Sent: Monday, April 6, 2020 11:49 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error in Tracula-all -prep
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Hi Freesurfer community,
I have an issue that I spent ages trying to figure out and this error has been asked about back in (17/12/2016) and the title is ([Freesurfer] Tracula trac -all preprocessing error.
my error is:
ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni
There is an issue that the mini folder is empty.
Attached is the log file and the configuration file (tracula_conf.txt)
Regards, Salah