Hi Rosalia
once you have imported the data for a subject with -i <input file>, you
shouldn't specify it for subsequent analyses
cheers
Bruce
On Fri, 19 Oct 2018, Rosalia Dacosta
Aguayo wrote:
External Email - Use Caution
Dear FreeSurfer team,
I am trying to run recon -all -autorecon2 using the following command line:
recon-all -sd
~/Desktop/MS_STUDY/subjects -s 001 -i
/home/rosalia/Desktop/MS_STUDY/subjects/001 -autorecon2
It is the same command I used yesterday to run -autorecon1 without problems.
However, maybe now it
is different. Should I point to another sub folder? I do not know which -i I
should point out now.
My directory for this subject is as follows:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $ ls
brainmask.auto.mgz nu.mgz rawavg.mgz
brainmask.mgz orig T1.mgz
mri_nu_correct.mni.log orig.mgz talairach_with_skull.log
mri_nu_correct.mni.log.bak orig_nu.mgz transforms
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $
Best regards,
Rosalia
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
