Is CON_101.nii in the/home/kumarlab/Downloads/Freesurfer_VBM folder? If not, you must specify the full path to the the file
On 12/15/2016 06:26 PM, 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 > > > > > > > Regards > /Sadhana Singh, PhD / > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
