it should not change the quality of the subcortical or cortical streams at all. the talairach.xfm is used for reporting purposes in the gui tools, and for group averaging (in some instances, qdec not being one of them). so i would not worry about introducing a bias. if you are concerned about a bias, the thing to do (which ought to be done as a QA step anyway) is to run:
tkregister --s <subjid> --fstal --surfs on all your subjects after recon-all has finished (or after -autorecon1 as long as you exclude the --surfs flag) and make sure the alignment is 'good enough'. n. On Wed, 2011-11-02 at 16:22 -0400, Joshua Lee wrote: > OK, now I understand better. > One further question: Would the use of MRI-total degrade quality of > the Freesurfer segmentations substantively, and would using it only on > a portion of my data introduce a systematic bias to the data set? > Josh > > > > > On Wed, Nov 2, 2011 at 4:15 PM, Nick Schmansky > <ni...@nmr.mgh.harvard.edu> wrote: > no, v5.0 uses nu.mgz as input to the talairach_avi routine, > whereas v5.1 > uses orig.mgz. > > its hard to say why it would fail for some subjects but not > others, > other than head positioning and to some degree ventricle size > makes a > difference. > > n. > > > On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote: > > Thanks Nick, > > > > Is use-mritotal equivalent to what version 5.0 does by > default? > > > > Also, any suggestions on why this talairach error would > occur only on > > a portion of my data, despite all being collected with the > same > > imaging protocol, same conversions from dicom, etc? > > - > > > > Joshua Lee > > > > Graduate Student > > Center for Mind and Brain & > > > > Department of Psychology > > > > University of California, Davis > > 530.747.3805 > > > > > > On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky > > <ni...@nmr.mgh.harvard.edu> wrote: > > joshua, > > > > try adding -use-mritotal to the end of your > recon-all > > command. it will > > use an alternate way to compute the talairach.xfm > which works > > better on > > some data. > > > > the change from v5.0 to v5.1 in the talairach stage > was that > > in v5.1, > > the talairach.xfm is needed to compute nu.mgz, so > the > > talairach stage > > needs to precede the nu_correct stage. this means > the > > talairach stage > > can no longer use nu.mgz as input, which seems to > work better > > than > > orig.mgz for some data (and is the case for your > data). > > > > in the next release of freesurfer, recon-all will > > automatically try the > > alternate method (mritotal) if the default > talairach_avi > > method fails > > the tal-check. > > > > n. > > > > > > > > On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl > wrote: > > > can you send us an example that works in 5.0 and > fails in > > 5.1? > > > > > > thanks > > > Bruce > > > On Wed, 2 Nov > > > 2011, Joshua Lee wrote: > > > > > > > Small Update: Error Disappears if Using > Freesurfer version > > 5.0 instead of > > > > 5.1. However, since I am keenly interested in > the > > hippocampal-subfield > > > > segmentation capabilities of the most recent > version, I am > > loathe to regress > > > > to an earlier version of FreeSurfer > > > > - > > > > Joshua Lee > > > > Graduate Student > > > > Center for Mind and Brain & > > > > Department of Psychology > > > > University of California, Davis > > > > 530.747.3805 > > > > > > > > > > > > On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee > > <jki...@ucdavis.edu> wrote: > > > > #@# Talairach Failure Detection Wed Nov 2 > 02:03:32 > > EDT 2011 > > > > > /home/virtualuser/freesurfer/subjects/test005/mri > > > > > > > > talairach_afd -T 0.005 -xfm > > transforms/talairach.xfm > > > > > > > > I am receiving the error (pasted below) on > about > > half of my > > > > scans, despite all cans using same > protocol. I > > detect no obvious > > > > issue with the quality of the images. I > have > > original dicoms, > > > > and am using mri_convert to save into a > single .mgz > > (or .nii, > > > > doesn't neem to make a difference), and > the > > unpredictability of > > > > the error makes diagnosis problematic. > TKMedit2 > > reveals > > > > absolutely wacky registrations. I am > processing on > > Freesurfer > > > > 5.1, and have replicated issue on two > different > > installations. I > > > > am designing a new longitudinal study > inheriting the > > same > > > > imaging protocol and I do not want to get > in a > > situation > > > > demanding manual editing of the talairach. > Can > > anyone help me > > > > out? Thanks, Joshua > > > > > > > > ERROR: talairach_afd: Talairach Transform: > > > > transforms/talairach.xfm ***FAILED*** > (p=0.0030, > > pval=0.0000 < > > > > threshold=0.0050) > > > > Manual Talairach alignment may be > necessary, or > > > > include the -notal-check flag to skip this > test, > > > > making sure the -notal-check flag follows > -all > > > > or -autorecon1 in the command string. > > > > See > > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > > > Linux FreeSurfer 2.6.28-11-generic > #42-Ubuntu SMP > > Fri Apr 17 > > > > 01:57:59 UTC 2009 i686 GNU/Linux > > > > > > > > recon-all -s test005 exited with ERRORS at > Wed Nov > > 2 02:03:32 > > > > EDT 2011 > > > > > > > > For more details, see the log file > > > > > > > /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log > > > > To report a problem, see > > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > - > > > > Joshua Lee > > > > Graduate Student > > > > Center for Mind and Brain & > > > > Department of Psychology > > > > University of California, Davis > > > > 530.747.3805 > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > 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. > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
