Hi Bruce,
I found on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Fixing Bad Output From the Talairach Registration
FreeSurfer computes a linear Talairach transform contained in a 3x4 matrix in a file called talairach.xfm and is located in the <subject name>/mri/transforms directory. Under some circumstances, the alignment can *fail the automatic failure detection scheme* (-tal-check flag, which can be disabled via -notal-check). Indeed, when I run recon-all with -notal-check, I donot see:
*#@# Talairach Failure Detection Wed Apr 6 12:36:53 EDT 2011 in recon-all-staus.log file any more.
Does this mean I have to do the manual talairach registration every time I run my recon-all, as it is a time consuming process? Is there any thing (from an acquisition perspective or otherwise) to eliminate this problem?
Thanks in advance.
On Thu, Apr 7, 2011 at 12:27 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
but you don't know what else was running on the same node at the time, do you? Can you lock the amount of memory you will need? I think to be safe you want 3G, but maybe Nick can chime in
On Thu, 7 Apr 2011, Saad Ramadan wrote:
Hi Bruce,
it is a cluster here a Brigham and wouldnot expect it to be low on memory. When I run a shell: free -mt
I get:
total used free shared bufferscached Mem: 3950 2918 1031 0 163 1596 -/+ buffers/cache: 1158 2791 Swap: 3820 125 3694 Total: 7770 3044 4725
On Thu, Apr 7, 2011 at 10:52 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
how much memory do you have in that machine?
Bruce
On Thu, 7 Apr 2011, Saad Ramadan wrote:
Dear all,
I ran (on an isotropic MPRAGE ):
recon-all -subject mysubject -i ./DICOM/test.25.1.2010.04.27.21.51.18.31250.14004670.IMA -autorecon-all
which ran for few hours and then exited without a successful end as can be seen on log file below.
Contents of *recon-all-status.log* are:
Wed Apr 6 12:31:55 EDT 2011 #@# MotionCor Wed Apr 6 12:33:10 EDT 2011 #@# Nu Intensity Correction Wed Apr 6 12:33:40 EDT 2011 #@# Talairach Wed Apr 6 12:35:22 EDT 2011 *#@# Talairach Failure Detection Wed Apr 6 12:36:53 EDT 2011 *#@# Intensity Normalization Wed Apr 6 12:36:53 EDT 2011 #@# Skull Stripping Wed Apr 6 12:41:44 EDT 2011 #@# EM Registration Wed Apr 6 14:16:04 EDT 2011 #@# CA Normalize Wed Apr 6 15:18:54 EDT 2011 #@# CA Reg Wed Apr 6 15:22:59 EDT 2011
The last few lines of *recon-all.log* produces:
0091: dt=0.112000, rms=0.700 (-0.001%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.638, neg=0, invalid=766 0092: dt=0.772947, rms=0.623 (2.335%), neg=0, invalid=766 0093: dt=0.028000, rms=0.622 (0.145%), neg=0, invalid=766 0094: dt=0.028000, rms=0.622 (-0.063%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=766
Do you have any idea what is going wrong here?
Thanks
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Hi Saad,
why do you think that the talairach was a problem? That wasn't what was failing in your previous email
Bruce On Thu, 7 Apr 2011, Saad Ramadan wrote:
Hi Bruce,
I found on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Fixing Bad Output From the Talairach Registration
FreeSurfer computes a linear Talairach transform contained in a 3x4 matrix in a file called talairach.xfm and is located in the <subject name>/mri/transforms directory. Under some circumstances, the alignment can *fail the automatic failure detection scheme* (-tal-check flag, which can be disabled via -notal-check). Indeed, when I run recon-all with -notal-check, I donot see:
*#@# Talairach Failure Detection Wed Apr 6 12:36:53 EDT 2011 in recon-all-staus.log file any more.
Does this mean I have to do the manual talairach registration every time I run my recon-all, as it is a time consuming process? Is there any thing (from an acquisition perspective or otherwise) to eliminate this problem?
Thanks in advance.
On Thu, Apr 7, 2011 at 12:27 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
but you don't know what else was running on the same node at the time, do you? Can you lock the amount of memory you will need? I think to be safe you want 3G, but maybe Nick can chime in
On Thu, 7 Apr 2011, Saad Ramadan wrote:
Hi Bruce,
it is a cluster here a Brigham and wouldnot expect it to be low on memory. When I run a shell: free -mt
I get:
total used free shared bufferscached Mem: 3950 2918 1031 0 163 1596 -/+ buffers/cache: 1158 2791 Swap: 3820 125 3694 Total: 7770 3044 4725
On Thu, Apr 7, 2011 at 10:52 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
how much memory do you have in that machine?
Bruce
On Thu, 7 Apr 2011, Saad Ramadan wrote:
Dear all,
I ran (on an isotropic MPRAGE ):
recon-all -subject mysubject -i ./DICOM/test.25.1.2010.04.27.21.51.18.31250.14004670.IMA -autorecon-all
which ran for few hours and then exited without a successful end as can be seen on log file below.
Contents of *recon-all-status.log* are:
Wed Apr 6 12:31:55 EDT 2011 #@# MotionCor Wed Apr 6 12:33:10 EDT 2011 #@# Nu Intensity Correction Wed Apr 6 12:33:40 EDT 2011 #@# Talairach Wed Apr 6 12:35:22 EDT 2011 *#@# Talairach Failure Detection Wed Apr 6 12:36:53 EDT 2011 *#@# Intensity Normalization Wed Apr 6 12:36:53 EDT 2011 #@# Skull Stripping Wed Apr 6 12:41:44 EDT 2011 #@# EM Registration Wed Apr 6 14:16:04 EDT 2011 #@# CA Normalize Wed Apr 6 15:18:54 EDT 2011 #@# CA Reg Wed Apr 6 15:22:59 EDT 2011
The last few lines of *recon-all.log* produces:
0091: dt=0.112000, rms=0.700 (-0.001%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.638, neg=0, invalid=766 0092: dt=0.772947, rms=0.623 (2.335%), neg=0, invalid=766 0093: dt=0.028000, rms=0.622 (0.145%), neg=0, invalid=766 0094: dt=0.028000, rms=0.622 (-0.063%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=766
Do you have any idea what is going wrong here?
Thanks
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
-
Bruce Fischl -
Saad Ramadan