Are the MNI tools in your path?

Harshad Shanbhag wrote:

Hi all,

I am trying to use FreeSurfer to overlay FSL data.

On running the command $ recon-all -stage1 -subjid TEST

I get the following error,

Nu Intensity Correction Tue Mar 1 14:54:08 EST 2005 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=1.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc nu_correct: Command not found. ERROR: nu_correct

I do have MNI Tools installed, in the freesurfer folder.

Please let me know what I should do.

Thank you. Harshad. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer