well, you specified -autorecon3, which assumes some stuff has been run
before. If you want to do everything from beginning to end run -all instead
Bruce
On Fri, 23 Jun 2006, Anil Roy wrote:
This is the first step. I assumed that recon-all should do all the
processing by itself without the need to run anything previously. Please
mention if any extra steps have to be taken before the parcellation stats
(or the entire recon-all process) can be obtained from the minc file.
Thanks - Anil.
On 6/23/06, Bruce Fischl <[EMAIL PROTECTED]> wrote:
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...
> #--------------------------------------------
> [EMAIL PROTECTED] 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
>
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