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
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