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
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
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
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
I tried using the -all option but I'm still getting an error. It runs for about 15 secs. I tried it on a different brain too but the error still remains.
# recon-all -i /root/Desktop/F200.mnc -subjid F200 -sd /usr/local/freesurfer/subjects -all
I've attached the output to a text file. Any help is greatly appreciated. Thanks - Anil Roy.
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
freesurfer@nmr.mgh.harvard.edu
-
Anil Roy -
Bruce Fischl