what steps have you run previously? You don't need to specify -i on later stages, just the subjid and sd.
On Fri, 23 Jun 2006, Anil Roy wrote:
Hello All,
So I tried using recon-all to get a few parcellations stats from a minc file it but I'm getting the following error. Please could someone say how this can be rectified. Thanks. - Anil Roy.
This is the command I'm giving:
# recon-all -force -i /root/Desktop/F100.mnc -subjid F100 -sd /usr/local/freesurfer/subjects -autorecon3
This is the output.
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects INFO: /usr/local/freesurfer/subjects/F100 exists with -i, but -force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 30123 Jun 23 15:50 /usr/local/freesurfer/subjects/F100/scripts/recon-all.log Linux dhcp-129-105-146-155.speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux WM removal version /usr/local/freesurfer/subjects/F100
mri_convert /root/Desktop/F100.mnc /usr/local/freesurfer/subjects/F100/mri/orig/001.mgz
mri_convert /root/Desktop/F100.mnc /usr/local/freesurfer/subjects/F100/mri/orig/001.mgz reading from /root/Desktop/F100.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/F100/mri/orig/001.mgz... #-------------------------------------------- #@# Sphere lh Fri Jun 23 15:56:29 CDT 2006 /usr/local/freesurfer/subjects/F100/scripts
mris_sphere ../surf/lh.inflated ../surf/lh.sphere
$Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ $Id: mrisurf.c,v 1.441.2.3 2006/04/12 02:03:02 nicks Exp $ MRISread(../surf/lh.inflated): could not open file No such file or directory mris_sphere: could not read surface file ../surf/lh.inflated No such file or directory Linux speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Fri Jun 23 15:56:29 CDT 2006