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

 

        External Email - Use Caution        

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

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