Dear all,
I get the same error when running any subject. I think it may be related to the step concerning: fsaverage/label/lh.BA1.label. I cannot detect where the problem is coming from. I thought that it was an issue with my environment, because there is a double slash in FREESURFER_HOME and all the other environments:
FREESURFER_HOME /usr/local//freesurfer FSFAST_HOME /usr/local//freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local//freesurfer/subjects MNI_DIR /usr/local//freesurfer/mni
but I just saw that this shouldn't be a problem (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012860....). Could you help me identify this error? I copy-pasted the output of bugr and other information. You will find attached also the recon-all.log of one of the subjects.
output of bugr: ---------------------------------------------------------------------
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
---------------------------------------------------------------------
1) subject name: it happens with any subject
2) the entire command-line executed recon-all -autorecon1 -autorecon2 -autorecon3 -i $g -s $subjid
where: $g = /path/to/nii/file and $subjid = subject ID
3) the error message generated from the recon-all.log:
SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local//freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s B_LU_02_MRI_E_T0 exited with ERRORS at Sat Nov 14 06:33:30 CET 2015
from the recon-all.error: $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local//freesurfer/bin/recon-all PWD /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label CMD mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject B_LU_02_MRI_E_T0 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
Best regards,
Max
Can you run:
ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label
and report the results?
cheers Bruce
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear all,
I get the same error when running any subject. I think it may be related to the step concerning: fsaverage/label/lh.BA1.label. I cannot detect where the problem is coming from. I thought that it was an issue with my environment, because there is a double slash in FREESURFER_HOME and all the other environments:
FREESURFER_HOME /usr/local//freesurfer FSFAST_HOME /usr/local//freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local//freesurfer/subjects MNI_DIR /usr/local//freesurfer/mni
but I just saw that this shouldn't be a problem (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012860....). Could you help me identify this error? I copy-pasted the output of bugr and other information. You will find attached also the recon-all.log of one of the subjects.
output of bugr:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
- subject name:
it happens with any subject
- the entire command-line executed
recon-all -autorecon1 -autorecon2 -autorecon3 -i $g -s $subjid
where: $g = /path/to/nii/file and $subjid = subject ID
- the error message generated
from the recon-all.log:
SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local//freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s B_LU_02_MRI_E_T0 exited with ERRORS at Sat Nov 14 06:33:30 CET 2015
from the recon-all.error: $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local//freesurfer/bin/recon-all PWD /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label CMD mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject B_LU_02_MRI_E_T0 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
Best regards,
Max
-- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg
maximila.bautista-perpinya@etu.unistra.fr
Dear Bruce,
# ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label ls: Kein Treffer. (meaning: no match)
# ls /usr/local/freesurfer/subjects/fsaverage ls: Zugriff auf /usr/local/freesurfer/subjects/fsaverage nicht möglich: Zu viele Ebenen aus symbolischen Links (meaning: access to /usr/local/freesurfer/subjects/fsaverage not possible: too many levels of symbolic links)
Best,
Max
On dijous 19 novembre 2015 15:03 CET, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Can you run:
ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label
and report the results?
cheers Bruce
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear all,
I get the same error when running any subject. I think it may be related to the step concerning: fsaverage/label/lh.BA1.label. I cannot detect where the problem is coming from. I thought that it was an issue with my environment, because there is a double slash in FREESURFER_HOME and all the other environments:
FREESURFER_HOME /usr/local//freesurfer FSFAST_HOME /usr/local//freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local//freesurfer/subjects MNI_DIR /usr/local//freesurfer/mni
but I just saw that this shouldn't be a problem (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012860....). Could you help me identify this error? I copy-pasted the output of bugr and other information. You will find attached also the recon-all.log of one of the subjects.
output of bugr:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
- subject name:
it happens with any subject
- the entire command-line executed
recon-all -autorecon1 -autorecon2 -autorecon3 -i $g -s $subjid
where: $g = /path/to/nii/file and $subjid = subject ID
- the error message generated
from the recon-all.log:
SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local//freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s B_LU_02_MRI_E_T0 exited with ERRORS at Sat Nov 14 06:33:30 CET 2015
from the recon-all.error: $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local//freesurfer/bin/recon-all PWD /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label CMD mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject B_LU_02_MRI_E_T0 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
Best regards,
Max
-- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg
maximila.bautista-perpinya@etu.unistra.fr
that means the FS version you have didn't have those labels. We can get you the entire set of BA labels, but you will need a new version of recon-all. Maybe your best bet is to insteall 6.0 beta and just run the -balabels target from it?
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear Bruce,
# ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label ls: Kein Treffer. (meaning: no match)
# ls /usr/local/freesurfer/subjects/fsaverage ls: Zugriff auf /usr/local/freesurfer/subjects/fsaverage nicht möglich: Zu viele Ebenen aus symbolischen Links (meaning: access to /usr/local/freesurfer/subjects/fsaverage not possible: too many levels of symbolic links)
Best,
Max
On dijous 19 novembre 2015 15:03 CET, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Can you run:
ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label
and report the results?
cheers Bruce
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear all,
I get the same error when running any subject. I think it may be related to the step concerning: fsaverage/label/lh.BA1.label. I cannot detect where the problem is coming from. I thought that it was an issue with my environment, because there is a double slash in FREESURFER_HOME and all the other environments:
FREESURFER_HOME /usr/local//freesurfer FSFAST_HOME /usr/local//freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local//freesurfer/subjects MNI_DIR /usr/local//freesurfer/mni
but I just saw that this shouldn't be a problem (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012860....). Could you help me identify this error? I copy-pasted the output of bugr and other information. You will find attached also the recon-all.log of one of the subjects.
output of bugr:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
- subject name:
it happens with any subject
- the entire command-line executed
recon-all -autorecon1 -autorecon2 -autorecon3 -i $g -s $subjid
where: $g = /path/to/nii/file and $subjid = subject ID
- the error message generated
from the recon-all.log:
SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local//freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s B_LU_02_MRI_E_T0 exited with ERRORS at Sat Nov 14 06:33:30 CET 2015
from the recon-all.error: $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local//freesurfer/bin/recon-all PWD /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label CMD mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject B_LU_02_MRI_E_T0 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
Best regards,
Max
-- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg
maximila.bautista-perpinya@etu.unistra.fr
Dear Bruce,
Thank you, I will try to do that, but I am not so clear about it. I should install the 6.0beta version of FS, but keep the one I have currently (v 1.379.2.73)? Then I should run with the 6.0beta version recon-all -balabels -i /path/to/file -s subjid; and then the complete recon-all with my current version? Is that right?
Best,
Max
On dijous 19 novembre 2015 15:35 CET, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
that means the FS version you have didn't have those labels. We can get you the entire set of BA labels, but you will need a new version of
recon-all. Maybe your best bet is to insteall 6.0 beta and just run the -balabels target from it?
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear Bruce,
# ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label ls: Kein Treffer. (meaning: no match)
# ls /usr/local/freesurfer/subjects/fsaverage ls: Zugriff auf /usr/local/freesurfer/subjects/fsaverage nicht möglich: Zu viele Ebenen aus symbolischen Links (meaning: access to /usr/local/freesurfer/subjects/fsaverage not possible: too many levels of symbolic links)
Best,
Max
On dijous 19 novembre 2015 15:03 CET, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Can you run:
ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label
and report the results?
cheers Bruce
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear all,
I get the same error when running any subject. I think it may be related to the step concerning: fsaverage/label/lh.BA1.label. I cannot detect where the problem is coming from. I thought that it was an issue with my environment, because there is a double slash in FREESURFER_HOME and all the other environments:
FREESURFER_HOME /usr/local//freesurfer FSFAST_HOME /usr/local//freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local//freesurfer/subjects MNI_DIR /usr/local//freesurfer/mni
but I just saw that this shouldn't be a problem (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012860....). Could you help me identify this error? I copy-pasted the output of bugr and other information. You will find attached also the recon-all.log of one of the subjects.
output of bugr:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
- subject name:
it happens with any subject
- the entire command-line executed
recon-all -autorecon1 -autorecon2 -autorecon3 -i $g -s $subjid
where: $g = /path/to/nii/file and $subjid = subject ID
- the error message generated
from the recon-all.log:
SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local//freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s B_LU_02_MRI_E_T0 exited with ERRORS at Sat Nov 14 06:33:30 CET 2015
from the recon-all.error: $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local//freesurfer/bin/recon-all PWD /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label CMD mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject B_LU_02_MRI_E_T0 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
Best regards,
Max
-- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg
maximila.bautista-perpinya@etu.unistra.fr
yes, that's pretty much it. Alternatively we could just give you all the current BA labels and the command lines need to run to map them from fsaverage to your subjects
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear Bruce,
Thank you, I will try to do that, but I am not so clear about it. I should install the 6.0beta version of FS, but keep the one I have currently (v 1.379.2.73)? Then I should run with the 6.0beta version recon-all -balabels -i /path/to/file -s subjid; and then the complete recon-all with my current version? Is that right?
Best,
Max
On dijous 19 novembre 2015 15:35 CET, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
that means the FS version you have didn't have those labels. We can get you the entire set of BA labels, but you will need a new version of
recon-all. Maybe your best bet is to insteall 6.0 beta and just run the -balabels target from it?
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear Bruce,
# ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label ls: Kein Treffer. (meaning: no match)
# ls /usr/local/freesurfer/subjects/fsaverage ls: Zugriff auf /usr/local/freesurfer/subjects/fsaverage nicht möglich: Zu viele Ebenen aus symbolischen Links (meaning: access to /usr/local/freesurfer/subjects/fsaverage not possible: too many levels of symbolic links)
Best,
Max
On dijous 19 novembre 2015 15:03 CET, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Can you run:
ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label
and report the results?
cheers Bruce
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear all,
I get the same error when running any subject. I think it may be related to the step concerning: fsaverage/label/lh.BA1.label. I cannot detect where the problem is coming from. I thought that it was an issue with my environment, because there is a double slash in FREESURFER_HOME and all the other environments:
FREESURFER_HOME /usr/local//freesurfer FSFAST_HOME /usr/local//freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local//freesurfer/subjects MNI_DIR /usr/local//freesurfer/mni
but I just saw that this shouldn't be a problem (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012860....). Could you help me identify this error? I copy-pasted the output of bugr and other information. You will find attached also the recon-all.log of one of the subjects.
output of bugr:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
- subject name:
it happens with any subject
- the entire command-line executed
recon-all -autorecon1 -autorecon2 -autorecon3 -i $g -s $subjid
where: $g = /path/to/nii/file and $subjid = subject ID
- the error message generated
from the recon-all.log:
SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local//freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s B_LU_02_MRI_E_T0 exited with ERRORS at Sat Nov 14 06:33:30 CET 2015
from the recon-all.error: $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local//freesurfer/bin/recon-all PWD /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label CMD mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject B_LU_02_MRI_E_T0 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
Best regards,
Max
-- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg
maximila.bautista-perpinya@etu.unistra.fr
Ok, i actually think it would be easier to have only one FS version. How could i get the BA labels (and all the other coontents of fsaverage) again?
Best,
Max
On dijous 19 novembre 2015 15:51 CET, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
yes, that's pretty much it. Alternatively we could just give you all the current BA labels and the command lines need to run to map them from fsaverage to your subjects
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear Bruce,
Thank you, I will try to do that, but I am not so clear about it. I should install the 6.0beta version of FS, but keep the one I have currently (v 1.379.2.73)? Then I should run with the 6.0beta version recon-all -balabels -i /path/to/file -s subjid; and then the complete recon-all with my current version? Is that right?
Best,
Max
On dijous 19 novembre 2015 15:35 CET, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
that means the FS version you have didn't have those labels. We can get you the entire set of BA labels, but you will need a new version of
recon-all. Maybe your best bet is to insteall 6.0 beta and just run the -balabels target from it?
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear Bruce,
# ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label ls: Kein Treffer. (meaning: no match)
# ls /usr/local/freesurfer/subjects/fsaverage ls: Zugriff auf /usr/local/freesurfer/subjects/fsaverage nicht möglich: Zu viele Ebenen aus symbolischen Links (meaning: access to /usr/local/freesurfer/subjects/fsaverage not possible: too many levels of symbolic links)
Best,
Max
On dijous 19 novembre 2015 15:03 CET, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Can you run:
ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label
and report the results?
cheers Bruce
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear all,
I get the same error when running any subject. I think it may be related to the step concerning: fsaverage/label/lh.BA1.label. I cannot detect where the problem is coming from. I thought that it was an issue with my environment, because there is a double slash in FREESURFER_HOME and all the other environments:
FREESURFER_HOME /usr/local//freesurfer FSFAST_HOME /usr/local//freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local//freesurfer/subjects MNI_DIR /usr/local//freesurfer/mni
but I just saw that this shouldn't be a problem (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012860....). Could you help me identify this error? I copy-pasted the output of bugr and other information. You will find attached also the recon-all.log of one of the subjects.
output of bugr:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
- subject name:
it happens with any subject
- the entire command-line executed
recon-all -autorecon1 -autorecon2 -autorecon3 -i $g -s $subjid
where: $g = /path/to/nii/file and $subjid = subject ID
- the error message generated
from the recon-all.log:
SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local//freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s B_LU_02_MRI_E_T0 exited with ERRORS at Sat Nov 14 06:33:30 CET 2015
from the recon-all.error: $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local//freesurfer/bin/recon-all PWD /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label CMD mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject B_LU_02_MRI_E_T0 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
Best regards,
Max
-- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg
maximila.bautista-perpinya@etu.unistra.fr
freesurfer@nmr.mgh.harvard.edu
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BAUTISTA-PERPINYA Maximilia (ETU VIE) -
Bruce Fischl