Hi Sadhana

is the file CON_101.nii or CON_101.nii.gz? If the latter, you should give that to recon-all. There is also no need to convert to nifti - you can give recon-all a *single* file in the correct dicom series and it will happily to its thing

cheers Bruce On Thu, 15 Dec 2016, Sadhana Singh wrote:

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

RegardsSadhana Singh, PhD