Hi Rashmi
can you try 5.3 and see if it works? Alternatively you can email me the orig.mgz and I can try it Bruce On Wed, 30 Oct 2013, Rashmi Singh wrote:
Hey Bruce, I ran FreeSurfer recon -all (with flags -use-mritotal and -notal-check flags) with a data set that failed showing the same error that I had received earlier. I am sure have the correct data set. I am attaching the recon-all.log and the data. We have FreeSurfer Version 5.1.0 Please advice. Thanks, Rashmi
On 10/23/13 9:06 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Rashmi
what version are you running? If 5.3, upload the subject and I'll take a look Bruce On Tue, 22 Oct 2013, Rashmi Singh wrote:
Hello FreeSurfer experts, I am trying to run recon all on my data set, but I got following error message. Please help me understand the message and suggest solution. Thanks, Rashmi
#@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013
/home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/ANAL2013/CombT1T 2Practice/FreeSurfer/AA470-2prac/ mri
mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros)
spacing=8, using 3481 sample points, tol=1.00e-05...
register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (130, 148, 130) --> (130, 148, 130) using (130, 148, 130) as brain centroid... mean wm in atlas = 126, using box (130,148,130) --> (129, 147,129) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux enders 2.6.32-52-server #114-Ubuntu SMP Wed Sep 11 19:06:34 UTC 2013 x86_64 GNU/Linux
recon-all -s AA470-2prac exited with ERRORS at Tue Oct 22 13:57:26 CDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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.
Dear Bruce and others, As my server has a bad graphic card, so I want to install freesurfer in my computer. My computer can support OpenGL, and I installed ubuntu as I didnot know how to setup the graphic card driver in CentOS(I didnot know whether it was needed to setup). I completed the freeesurfer license and configured the bashrc. Then I ran the freesurfer command, such as freeview, but it told me that permission denied. So I "chmod 777 -R freesurfer", but it still told me "permission denied". My system is "ubuntu1310desktopamd64". Bruce, or others, would you please help me? All what I have done is to visualize the overlay,underlay and annotation in freeview but my server cannot do that. Thanks. All the best.
2013-12-27
Rujing Zha
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2013-10-31 03:58 主题：Re: [Freesurfer] reconall error 收件人："Rashmi Singh"rsingh@laureateinstitute.org 抄送："freesurfer@nmr.mgh.harvard.edu"freesurfer@nmr.mgh.harvard.edu
Hi Rashmi
can you try 5.3 and see if it works? Alternatively you can email me the orig.mgz and I can try it Bruce On Wed, 30 Oct 2013, Rashmi Singh wrote:
Hey Bruce, I ran FreeSurfer recon -all (with flags -use-mritotal and -notal-check flags) with a data set that failed showing the same error that I had received earlier. I am sure have the correct data set. I am attaching the recon-all.log and the data. We have FreeSurfer Version 5.1.0 Please advice. Thanks, Rashmi
On 10/23/13 9:06 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Rashmi
what version are you running? If 5.3, upload the subject and I'll take a look Bruce On Tue, 22 Oct 2013, Rashmi Singh wrote:
Hello FreeSurfer experts, I am trying to run recon all on my data set, but I got following error message. Please help me understand the message and suggest solution. Thanks, Rashmi
#@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013
/home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/ANAL2013/CombT1T 2Practice/FreeSurfer/AA470-2prac/ mri
mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros)
spacing=8, using 3481 sample points, tol=1.00e-05...
register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (130, 148, 130) --> (130, 148, 130) using (130, 148, 130) as brain centroid... mean wm in atlas = 126, using box (130,148,130) --> (129, 147,129) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux enders 2.6.32-52-server #114-Ubuntu SMP Wed Sep 11 19:06:34 UTC 2013 x86_64 GNU/Linux
recon-all -s AA470-2prac exited with ERRORS at Tue Oct 22 13:57:26 CDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Rujing
what directory did you run the chmod from? You are probably better off running:
chmod a+rx $FREESURFER_HOME/bin/*
see if that works. If not check yout path to make sure it includes that dir
cheers Bruce
On Fri, 27 Dec 2013, Rujing Zha wrote:
Dear Bruce and others, As my server has a bad graphic card, so I want to install freesurfer in my computer. My computer can support OpenGL, and I installed ubuntu as I didnot know how to setup the graphic card driver in CentOS(I didnot know whether it was needed to setup). I completed the freeesurfer license and configured the bashrc. Then I ran the freesurfer command, such as freeview, but it told me that permission denied. So I "chmod 777 -R freesurfer", but it still told me "permission denied". My system is "ubuntu1310desktopamd64". Bruce, or others, would you please help me? All what I have done is to visualize the overlay,underlay and annotation in freeview but my server cannot do that. Thanks. All the best. 2013-12-27
Rujing Zha
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2013-10-31 03:58 主题：Re: [Freesurfer] reconall error 收件人："Rashmi Singh"rsingh@laureateinstitute.org 抄送："freesurfer@nmr.mgh.harvard.edu"freesurfer@nmr.mgh.harvard.edu Hi Rashmi can you try 5.3 and see if it works? Alternatively you can email me the orig.mgz and I can try it Bruce On Wed, 30 Oct 2013, Rashmi Singh wrote:
Hey Bruce, I ran FreeSurfer recon -all (with flags -use-mritotal and -notal-check flags) with a data set that failed showing the same error that I had received earlier. I am sure have the correct data set. I am attaching the recon-all.log and the data. We have FreeSurfer Version 5.1.0 Please advice. Thanks, Rashmi On 10/23/13 9:06 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Rashmi what version are you running? If 5.3, upload the subject and I'll take a
look Bruce On Tue, 22 Oct 2013, Rashmi Singh wrote:
Hello FreeSurfer experts, I am trying to run recon all on my data set, but I got following error
?? ?>>> message.
Please help me understand the message and suggest solution. Thanks, Rashmi #@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013 /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/ANAL2013/CombT
1T
2Practice/FreeSurfer/AA470-2prac/ mri mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (130, 148, 130) --> (130, 148, 130) using (130, 148, 130) as brain centroid... mean wm in atlas = 126, using box (130,148,130) --> (129, 147,129) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux enders 2.6.32-52-server #114-Ubuntu SMP Wed Sep 11 19:06:34 UTC 2013 x86_64 GNU/Linux recon-all -s AA470-2prac exited with ERRORS at Tue Oct 22 13:57:26 CDT
?? ?>>> 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
The information in this e-mail is intended only for the person to whom i
t
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%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
n
error but does not contain patient information, please contact the sender and
?? ?>> properly
dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Rujing Zha