Hi I am using freesurfer for calculation cortical thickness in my subjects.
Firstly, I have converted all the T1 weighted images from dcm into nii.gz format. After that, I have run the recon-all in one subject using this script 'recon-all -i CON_101.nii -s CON_101 -all' , but it shows error The error is: [kumarlab@lcmodel ~]$ cd /home/kumarlab/Downloads/ Freesurfer_VBM [kumarlab@lcmodel Freesurfer_VBM]$ export SUBJECTS_DIR=/home/kumarlab/ Downloads/Freesurfer_VBM [kumarlab@lcmodel Freesurfer_VBM]$ recon-all -i CON_101.nii -s CON_101 -all ERROR: cannot find CON_101.nii Linux lcmodel 3.10.0-327.el7.x86_64 #1 SMP Thu Oct 29 17:29:29 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Thu Dec 15 16:14:29 EST 2016 Regards *Sadhana Singh, PhD *
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