Hi all,
I'm having a similar issue to the one described below - the mri_cc step seems stuck and goes on for days (still going); I'm using FreeSurfer version 5.1 as well. Like Bruce said in another thread, this could be due to an empty norm.mgz file. This seems like it is my exact problem, as that file is empty. Is there a way to skip this step, or to re-run from autorecon1 and ensure the norm.mgz file is created?
Thanks, Adam
*Adam Mezher*
Staff Research Associate II
Center for Imaging of Neurodegenerative Diseases
San Francisco VA Medical Center
4150 Clement St. (114M)
San Francisco, CA 94121
Tel: 415-221-4810 Ext. 4629
Fax: 415-668-2864
If someone can send us and example of this behavior I will fix it Cheers Bruce
On Feb 20, 2013, at 12:23 PM, Matt Glasser <matt at ma-tea.com https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> wrote:
- I've noticed this at well when something goes wrong before mri_cc. It gets stuck in some kind of infinite loop. You might check that the linear and nonlinear registration worked correctly.
*> >* Peace, *> >* Matt. *> >* From: Dawei Liu <ldw70171 at gmail.com https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>* Date: Wednesday, February 20, 2013 10:49 AM *>* To: <freesurfer at nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>* Subject: [Freesurfer] unusually long running time in autorecon2 *> >* Dear Freesurfer experts, *> > > >* I am running autorecon2 using Freesurfer verion 5.1.0 on Linux. For some subjects, it looks that the pipeline stucked in the middle of mri_cc and keeps running for days (without any error message). Last time when it occurred I thought it may be caused by some hardware-related problem, so I killed these jobs and re-launched recon-all -autorecon2 on a different machine. Now these jobs have been running for over 40 hours and they are still running. Do you know why they take so long? For your reference, I copied the most recent processing information below: *> > > >* mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta 0057_34479 *> > > >* will read input aseg from aseg.auto_noCCseg.mgz *> >* writing aseg with cc labels to aseg.auto.mgz *> >* will write lta as /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta *> >* reading aseg from /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/aseg.auto_noCCseg.mgz *> >* reading norm from /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/norm.mgz *> >* 24076 voxels in left wm, 23641 in right wm, xrange [73, 130] *> >* searching rotation angles z=[65 79], y=[-54 -40] *> >* searching scale 1 Z rot 75.6 global minimum found at slice 103.0, rotations (-50.09, 68.60) *> >* final transformation (x=103.0, yr=-50.093, zr=68.597): *> >* 0.234 -0.931 -0.280 230.831; *> >* 0.597 0.365 -0.714 75.219; *> >* 0.767 -0.000 0.642 3.440; *> >* 0.000 0.000 0.000 1.000; *> > > >* Thanks in advance for your help! *> > > >* Dawei*
Hi Adam
yes, this is mri_cc in an infinite loop. This bug is fixed in 5.3, but it won't generate anything reasonable with an empty input volume. Do you know why it is blank? Is the brainmask.mgz ok? The talariach.lta and .xfm?
cheers Bruce
On Fri, 6 Dec 2013, Adam Mezher wrote:
Hi all,
I'm having a similar issue to the one described below - the mri_cc step seems stuck and goes on for days (still going); I'm using FreeSurfer version 5.1 as well. Like Bruce said in another thread, this could be due to an empty norm.mgz file. This seems like it is my exact problem, as that file is empty. Is there a way to skip this step, or to re-run from autorecon1 and ensure the norm.mgz file is created?
Thanks, Adam
Adam Mezher
Staff Research Associate II
Center for Imaging of Neurodegenerative Diseases
San Francisco VA Medical Center
4150 Clement St. (114M)
San Francisco, CA 94121
Tel: 415-221-4810 Ext. 4629
Fax: 415-668-2864
If someone can send us and example of this behavior I will fix it Cheers Bruce
On Feb 20, 2013, at 12:23 PM, Matt Glasser <MailScanner has detected a possi ble fraud attempt from "mail.nmr.mgh.harvard.edu" claiming to be matt at ma- tea.com> wrote:
I've noticed this at well when something goes wrong before mri_cc. It get
s stuck in some kind of infinite loop. You might check that the linear and nonlinear registration worked correctly.
Peace,
Matt.
From: Dawei Liu <MailScanner has detected a possible fraud attempt from "m
ail.nmr.mgh.harvard.edu" claiming to be ldw70171 at gmail.com>
Date: Wednesday, February 20, 2013 10:49 AM To: <freesurfer at nmr.mgh.harvard.edu> Subject: [Freesurfer] unusually long running time in autorecon2
Dear Freesurfer experts,
I am running autorecon2 using Freesurfer verion 5.1.0 on Linux. For some s
ubjects, it looks that the pipeline stucked in the middle of mri_cc and kee ps running for days (without any error message). Last time when it occurred I thought it may be caused by some hardware-related problem, so I killed the se jobs and re-launched recon-all -autorecon2 on a different machine. Now th ese jobs have been running for over 40 hours and they are still running. Do you know why they take so long? For your reference, I copied the most recen t processing information below:
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Experiments/2012
0801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/transforms /cc_up.lta 0057_34479
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as /Experiments/20120801.SubjectOrganized_Results/20121213_
RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta
reading aseg from /Experiments/20120801.SubjectOrganized_Results/20121213_
RAW_T1_ONLY/0057_34479/mri/aseg.auto_noCCseg.mgz
reading norm from /Experiments/20120801.SubjectOrganized_Results/20121213_
RAW_T1_ONLY/0057_34479/mri/norm.mgz
24076 voxels in left wm, 23641 in right wm, xrange [73, 130]
searching rotation angles z=[65 79], y=[-54 -40]
searching scale 1 Z rot 75.6 global minimum found at slice 103.0, rotatio
ns (-50.09, 68.60)
final transformation (x=103.0, yr=-50.093, zr=68.597):
0.234 -0.931 -0.280 230.831;
0.597 0.365 -0.714 75.219;
0.767 -0.000 0.642 3.440;
0.000 0.000 0.000 1.000;
Thanks in advance for your help!
Dawei
Hi Bruce,
I'm not too sure why it is blank, the talairach.lta and .xfm look fine to me (but I could be mistaken, see below). The brainmask.mgz is actually quite grainy but I'm not sure if that alone would contribute to this issue.
# transform file transforms/talairach.lta # created by vhasfcngp on Thu Dec 5 10:52:15 2013
type = 0 nxforms = 1 mean = 124.0000 128.0000 113.0000 sigma = 10000.0000 1 4 4 1.015566825866699e+00 3.688731789588928e-02 -5.217729881405830e-02 -1.508542060852051e+00 -3.640308603644371e-02 1.072198033332825e+00 9.683787077665329e-02 -1.813611602783203e+01 6.455218791961670e-02 -6.284867227077484e-02 9.031718373298645e-01 7.219198703765869e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = nu.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = -5.897590637207031e+00 3.518244934082031e+01 7.421691894531250e+00 dst volume info valid = 1 # volume info valid filename = /opt/freesurfer5.1/average/RB_all_2008-03-26.gca volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
MNI Transform File % avi2talxfm
Transform_Type = Linear; Linear_Transform = 1.018529 0.026263 0.058106 2.694183 -0.014134 0.976859 0.266596 -38.123657 -0.048405 -0.219964 1.105566 -2.497101;
Thanks a lot, Adam
On Fri, Dec 6, 2013 at 10:52 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Adam
yes, this is mri_cc in an infinite loop. This bug is fixed in 5.3, but it won't generate anything reasonable with an empty input volume. Do you know why it is blank? Is the brainmask.mgz ok? The talariach.lta and .xfm?
cheers Bruce
On Fri, 6 Dec 2013, Adam Mezher wrote:
Hi all,
I'm having a similar issue to the one described below - the mri_cc step seems stuck and goes on for days (still going); I'm using FreeSurfer version 5.1 as well. Like Bruce said in another thread, this could be due to an empty norm.mgz file. This seems like it is my exact problem, as that file is empty. Is there a way to skip this step, or to re-run from autorecon1 and ensure the norm.mgz file is created?
Thanks, Adam
Adam Mezher
Staff Research Associate II
Center for Imaging of Neurodegenerative Diseases
San Francisco VA Medical Center
4150 Clement St. (114M)
San Francisco, CA 94121
Tel: 415-221-4810 Ext. 4629
Fax: 415-668-2864
If someone can send us and example of this behavior I will fix it Cheers Bruce
On Feb 20, 2013, at 12:23 PM, Matt Glasser <MailScanner has detected a possi ble fraud attempt from "mail.nmr.mgh.harvard.edu" claiming to be matt at ma- tea.com> wrote:
I've noticed this at well when something goes wrong before mri_cc. It
get s stuck in some kind of infinite loop. You might check that the linear and nonlinear registration worked correctly.
Peace, Matt. From: Dawei Liu <MailScanner has detected a possible fraud attempt
from "m ail.nmr.mgh.harvard.edu" claiming to be ldw70171 at gmail.com>
Date: Wednesday, February 20, 2013 10:49 AM To: <freesurfer at nmr.mgh.harvard.edu> Subject: [Freesurfer] unusually long running time in autorecon2
Dear Freesurfer experts,
I am running autorecon2 using Freesurfer verion 5.1.0 on Linux.
For some s ubjects, it looks that the pipeline stucked in the middle of mri_cc and kee ps running for days (without any error message). Last time when it occurred I thought it may be caused by some hardware-related problem, so I killed the se jobs and re-launched recon-all -autorecon2 on a different machine. Now th ese jobs have been running for over 40 hours and they are still running. Do you know why they take so long? For your reference, I copied the most recen t processing information below: > > > > mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Experiments/2012 0801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_ 34479/mri/transforms /cc_up.lta 0057_34479
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz will write lta as /Experiments/20120801.SubjectOrganized_Results/
20121213_ RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta
reading aseg from /Experiments/20120801.SubjectOrganized_Results/
20121213_ RAW_T1_ONLY/0057_34479/mri/aseg.auto_noCCseg.mgz
reading norm from /Experiments/20120801.SubjectOrganized_Results/
20121213_ RAW_T1_ONLY/0057_34479/mri/norm.mgz
24076 voxels in left wm, 23641 in right wm, xrange [73, 130] searching rotation angles z=[65 79], y=[-54 -40] searching scale 1 Z rot 75.6 global minimum found at slice 103.0,
rotatio ns (-50.09, 68.60)
final transformation (x=103.0, yr=-50.093, zr=68.597): 0.234 -0.931 -0.280 230.831; 0.597 0.365 -0.714 75.219; 0.767 -0.000 0.642 3.440; 0.000 0.000 0.000 1.000;
Thanks in advance for your help! Dawei
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
if you upload the subject I'll take a look On Fri, 6 Dec 2013, Adam Mezher wrote:
Hi Bruce,
I'm not too sure why it is blank, the talairach.lta and .xfm look fine to me (but I could be mistaken, see below). The brainmask.mgz is actually quite grainy but I'm not sure if that alone would contribute to this issue.
# transform file transforms/talairach.lta # created by vhasfcngp on Thu Dec 5 10:52:15 2013
type = 0 nxforms = 1 mean = 124.0000 128.0000 113.0000 sigma = 10000.0000 1 4 4 1.015566825866699e+00 3.688731789588928e-02 -5.217729881405830e-02 -1.508542060852051e+00 -3.640308603644371e-02 1.072198033332825e+00 9.683787077665329e-02 -1.813611602783203e+01 6.455218791961670e-02 -6.284867227077484e-02 9.031718373298645e-01 7.219198703765869e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = nu.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = -5.897590637207031e+00 3.518244934082031e+01 7.421691894531250e+00 dst volume info valid = 1 # volume info valid filename = /opt/freesurfer5.1/average/RB_all_2008-03-26.gca volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
MNI Transform File % avi2talxfm
Transform_Type = Linear; Linear_Transform = 1.018529 0.026263 0.058106 2.694183 -0.014134 0.976859 0.266596 -38.123657 -0.048405 -0.219964 1.105566 -2.497101;
Thanks a lot, Adam
On Fri, Dec 6, 2013 at 10:52 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Adam
yes, this is mri_cc in an infinite loop. This bug is fixed in 5.3, but it won't generate anything reasonable with an empty input volume. Do you know why it is blank? Is the brainmask.mgz ok? The talariach.lta and .xfm? cheers Bruce On Fri, 6 Dec 2013, Adam Mezher wrote: Hi all, I'm having a similar issue to the one described below - the mri_cc step seems stuck and goes on for days (still going); I'm using FreeSurfer version 5.1 as well. Like Bruce said in another thread, this could be due to an empty norm.mgz file. This seems like it is my exact problem, as that file is empty. Is there a way to skip this step, or to re-run from autorecon1 and ensure the norm.mgz file is created? Thanks, Adam Adam Mezher Staff Research Associate II Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center 4150 Clement St. (114M) San Francisco, CA 94121 Tel: 415-221-4810 Ext. 4629 Fax: 415-668-2864 If someone can send us and example of this behavior I will fix it Cheers Bruce On Feb 20, 2013, at 12:23 PM, Matt Glasser <MailScanner has detected a possi ble fraud attempt from "mail.nmr.mgh.harvard.edu" claiming to be matt at ma- tea.com> wrote: > I've noticed this at well when something goes wrong before mri_cc. It get s stuck in some kind of infinite loop. You might check that the linear and nonlinear registration worked correctly. > > Peace, > > Matt. > > From: Dawei Liu <MailScanner has detected a possible fraud attempt from "m ail.nmr.mgh.harvard.edu" claiming to be ldw70171 at gmail.com> > Date: Wednesday, February 20, 2013 10:49 AM > To: <freesurfer at nmr.mgh.harvard.edu> > Subject: [Freesurfer] unusually long running time in autorecon2 > > Dear Freesurfer experts, > > > > I am running autorecon2 using Freesurfer verion 5.1.0 on Linux. For some s ubjects, it looks that the pipeline stucked in the middle of mri_cc and kee ps running for days (without any error message). Last time when it occurred I thought it may be caused by some hardware-related problem, so I killed the se jobs and re-launched recon-all -autorecon2 on a different machine. Now th ese jobs have been running for over 40 hours and they are still running. Do you know why they take so long? For your reference, I copied the most recen t processing information below: > > > > mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/transform s /cc_up.lta 0057_34479 > > > > will read input aseg from aseg.auto_noCCseg.mgz > > writing aseg with cc labels to aseg.auto.mgz > > will write lta as /Experiments/20120801.SubjectOrganized_Results/20121213_ RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta > > reading aseg from /Experiments/20120801.SubjectOrganized_Results/20121213_ RAW_T1_ONLY/0057_34479/mri/aseg.auto_noCCseg.mgz > > reading norm from /Experiments/20120801.SubjectOrganized_Results/20121213_ RAW_T1_ONLY/0057_34479/mri/norm.mgz > > 24076 voxels in left wm, 23641 in right wm, xrange [73, 130] > > searching rotation angles z=[65 79], y=[-54 -40] > > searching scale 1 Z rot 75.6 global minimum found at slice 103.0, rotatio ns (-50.09, 68.60) > > final transformation (x=103.0, yr=-50.093, zr=68.597): > > 0.234 -0.931 -0.280 230.831; > > 0.597 0.365 -0.714 75.219; > > 0.767 -0.000 0.642 3.440; > > 0.000 0.000 0.000 1.000; > > > > Thanks in advance for your help! > > > > Dawei
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Adam Mezher -
Bruce Fischl