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 <fis...@nmr.mgh.harvard.edu>wrote: > 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 buffers >> cached >> 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 <fis...@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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
