Freesurfer devs,
In freesurfer 6 stable I'm having a problem at the careg stage of the long. The relevant recon-all log is pasted below. Could you point me to where to debug this problem?
Cheers,
Chris.
mri_ca_register -rusage 136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.dat -bigventricles -smoothness 0.5 -levels 2 -A 1 -l *base*/transforms/talairach.m3z identity.nofile -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z
handling expanded ventricles... l_smoothness = 0.50 levels = 2 smoothing gradient with 1 averages... reading previously computed atlas xform /isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transforms/talairach.m3z and applying inverse registration identity.nofile renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_ca_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) TransformSample: gcam has not been inverted! freeing gibbs priors...done. average std[0] = 5.0 setting orig areas to linear transform determinant scaled 8.40 writing talairach.invalid.mgz writing talairach.status.mgz registering ventricular system... using threshold 45.0 from atlas ventricle (20.1 +- 5.0) and caudate (70.0 +- 5.0) distributions for initial ventricular estimate No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory
Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences
Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson@mcri.edu.aumailto:chris.adamson@mcri.edu.au www.mcri.edu.auhttp://www.mcri.edu.au/
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
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It happens when I use -bigventricles.
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson Sent: Thursday, 6 April 2017 12:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] long mri_ca_register error
Freesurfer devs,
In freesurfer 6 stable I'm having a problem at the careg stage of the long. The relevant recon-all log is pasted below. Could you point me to where to debug this problem?
Cheers,
Chris.
mri_ca_register -rusage 136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.dat -bigventricles -smoothness 0.5 -levels 2 -A 1 -l *base*/transforms/talairach.m3z identity.nofile -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z
handling expanded ventricles... l_smoothness = 0.50 levels = 2 smoothing gradient with 1 averages... reading previously computed atlas xform /isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transforms/talairach.m3z and applying inverse registration identity.nofile renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_ca_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) TransformSample: gcam has not been inverted! freeing gibbs priors...done. average std[0] = 5.0 setting orig areas to linear transform determinant scaled 8.40 writing talairach.invalid.mgz writing talairach.status.mgz registering ventricular system... using threshold 45.0 from atlas ventricle (20.1 +- 5.0) and caudate (70.0 +- 5.0) distributions for initial ventricular estimate No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory
Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences
Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson@mcri.edu.aumailto:chris.adamson@mcri.edu.au www.mcri.edu.auhttp://www.mcri.edu.au/
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
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Hi Chris
it's possible we never looked at -bigventricle in the long stage. What was your recon-all command line?
cheers Bruce On Thu, 6 Apr 2017, Chris Adamson wrote:
It happens when I use -bigventricles.
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson Sent: Thursday, 6 April 2017 12:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] long mri_ca_register error
Freesurfer devs,
In freesurfer 6 stable I’m having a problem at the careg stage of the long. The relevant recon-all log is pasted below. Could you point me to where to debug this problem?
Cheers,
Chris.
mri_ca_register -rusage 136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.dat -bigventricles -smoothness 0.5 -levels 2 -A 1 -l *base*/transforms/talairach.m3z identity.nofile -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z
handling expanded ventricles...
l_smoothness = 0.50
levels = 2
smoothing gradient with 1 averages...
reading previously computed atlas xform /isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transforms/talairach.m3z and applying inverse registration identity.nofile
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_ca_register for OpenMP = 2 ==
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
TransformSample: gcam has not been inverted!
freeing gibbs priors...done.
average std[0] = 5.0
setting orig areas to linear transform determinant scaled 8.40
writing talairach.invalid.mgz
writing talairach.status.mgz
registering ventricular system...
using threshold 45.0 from atlas ventricle (20.1 +- 5.0) and caudate (70.0 +- 5.0) distributions for initial ventricular estimate
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
Dr Chris Adamson
Senior Research Officer
Developmental Imaging, Clinical Sciences
Murdoch Childrens Research Institute
The Royal Children’s Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adamson@mcri.edu.au
www.mcri.edu.au
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
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Just the standard pipeline.
recon-all -s cross1 -all -bigventricles recon-all -base cross -tp cross1 ... -all -bigventricles recon-all -long cross1 cross -all -bigventricles
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, 7 April 2017 3:37 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long mri_ca_register error
Hi Chris
it's possible we never looked at -bigventricle in the long stage. What was your recon-all command line?
cheers Bruce On Thu, 6 Apr 2017, Chris Adamson wrote:
It happens when I use -bigventricles.
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson Sent: Thursday, 6 April 2017 12:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] long mri_ca_register error
Freesurfer devs,
In freesurfer 6 stable I’m having a problem at the careg stage of the long. The relevant recon-all log is pasted below. Could you point me to where to debug this problem?
Cheers,
Chris.
mri_ca_register -rusage 136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.dat -bigventricles -smoothness 0.5 -levels 2 -A 1 -l *base*/transforms/talairach.m3z identity.nofile -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z
handling expanded ventricles...
l_smoothness = 0.50
levels = 2
smoothing gradient with 1 averages...
reading previously computed atlas xform /isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transforms/talaira ch.m3z and applying inverse registration identity.nofile
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_ca_register for OpenMP = 2 ==
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
TransformSample: gcam has not been inverted!
freeing gibbs priors...done.
average std[0] = 5.0
setting orig areas to linear transform determinant scaled 8.40
writing talairach.invalid.mgz
writing talairach.status.mgz
registering ventricular system...
using threshold 45.0 from atlas ventricle (20.1 +- 5.0) and caudate (70.0 +- 5.0) distributions for initial ventricular estimate
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
Dr Chris Adamson
Senior Research Officer
Developmental Imaging, Clinical Sciences
Murdoch Childrens Research Institute
The Royal Children’s Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adamson@mcri.edu.au
www.mcri.edu.au
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
P Please consider the environment before printing this email
This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________
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If you have any questions, please contact MCRI IT Servicedesk for further assistance. ______________________________________________________________________
This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________
______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com
If you have any questions, please contact MCRI IT Servicedesk for further assistance. ______________________________________________________________________
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freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Chris Adamson