On 6/23/06, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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 <fischl@nmr.mgh.harvard.edu> 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...
>> > #--------------------------------------------
>> > #@# 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
>> >
>>
>