External Email - Use Caution

Try:

export TUTORIAL_DATA=/home/shao/tutorial_data

Tim

On August 11, 2020 at 6:51 AM Wei Shao wshao@research.baycrest.org wrote:

    External Email - Use Caution        

Hi, Freesurfer Team

My name is Wei Shao, I just a beginner of Freesurfer. As I play around with the tutorial data, here is a problem I met, I tried to recon-all the dicoms data as the tutorial instruction practice with the date instructed, but it always reports like the SUBJECTS_DIR directory does not exist.

[shao@WeiS ~]$ export TUTORIAL_DATA=tutorial_data [shao@WeiS ~]$ export SUBJECTS_DIR=$TUTORIAL_DATA/practice_with_data [shao@WeiS ~]$ cd $SUBJECTS_DIR/dicoms [shao@WeiS dicoms]$ recon-all -all -i I50 -s Subj001 ERROR: SUBJECTS_DIR tutorial_data/practice_with_data does not exist. [shao@WeiS dicoms]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: tutorial_data/practice_with_data does not exist FREESURFER_HOME /usr/local/freesurfer/7.1.0-1 FSFAST_HOME /usr/local/freesurfer/7.1.0-1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR tutorial_data/practice_with_data MNI_DIR /usr/local/freesurfer/7.1.0-1/mni [shao@WeiS dicoms]$ pwd /home/shao/tutorial_data/practice_with_data/dicoms [shao@WeiS dicoms]$

What I should do to fix this problem, Thanks in advance.

Best, Wei _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany