When you said to process it with the -notal-check to skip the talairach check....am I supposed to add that in the first recon all or add it to the recon all base command?
On 10/2/09 1:15 PM, "Martin Reuter" <mreu...@nmr.mgh.harvard.edu> wrote: Looks like the talairach check failed. Check the talairach.xfm (as you would do in the cross sectional processing, when this happens -> tutorial). If it looks OK try processing with -notal-check to skip the check. If it looks wrong, try to correct it with tkregister manually. Sometimes the transform is OK, but the check fails. Best, Martin On Fri, 2009-10-02 at 09:51 -0400, Weisinger, Brian (NIH/OD) [E] wrote: > I was running > > recon-all -base Sub1 -tp 00308 -tp 01150 -all > > After a couple of minutes it gave me this error message..... > > Fri Oct 2 09:48:05 EDT 2009 > talairach_avi done > \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n > #-------------------------------------------- > #...@# Talairach Failure Detection Fri Oct 2 09:48:06 EDT 2009 > /Applications/freesurfer/subjects/Sub1/mri > \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > Darwin CHP-MP2.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 > PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 > > recon-all exited with ERRORS at Fri Oct 2 09:48:06 EDT 2009 > > Any ideas how to fix this > > > > > > On 10/1/09 3:12 PM, "Martin Reuter" <mreu...@nmr.mgh.harvard.edu> wrote: > > Hi Brian, > > when you use the longitudinal stream in FreeSurfer, it accounts for the > 'relatedness' therefore the resulting information (e.g. segmentation > labels, volume measures, thickness measures, surface locations etc. ) > will be more accurate (on average) than if you'd just process the > different time points independently (cross sectionally). > > Comparing the results after FreeSurfer is through will work exactly the > same in both settings. You can compute what you are interested in (e.g. > percent volume loss in left hippocampus by looking into the aseg.stats , > or percent cortical thinning) per subject and then do a group analysis > with your two groups. > > Best, Martin > > > On Thu, 2009-10-01 at 14:39 -0400, Gogtay, Nitin (NIH/NIMH) [E] wrote: > > Hi Martin + others, > > > > Thank you for your help on this. > > > > I am still a bit confused and maybe you can help me understand. So we have > > a sample of 12 patients + 12 controls and each with 2 scans (time 1 and > > time 2) thus total 48 scans. > > > > As suggested these have been processed using the longitudinal free surfer > > algorithm (Thanks for your help regarding troubleshooting during that as > > well) > > > > To compare the results between two time points (I assume slopes of subjects > > compared to those of controls? And intercepts?), how does one account for > > the 'relatedness' i.e. Same subject two time points? As it is now, > > wouldn't the free surfer treat the data as 'cross sectional' to calculate > > the slopes? > > > > Maybe i/we are missing something? > > > > Sorry for the bother and thank you again for the help! > > > > Nitin > > > > Nitin Gogtay, M.D. > > Staff Clinician > > Child Psychiatry Branch, NIMH > > (301) 435 4494 > > > > ________________________________ > > From: "Weisinger, Brian (NIH/OD) [E]" <brian.weisin...@nih.gov> > > Date: Thu, 1 Oct 2009 14:26:23 -0400 > > To: Nitin Gogtay <gogt...@mail.nih.gov> > > Subject: FW: [Freesurfer] How to calculate differences using the > > longitudinal data > > > > > > ------ Forwarded Message > > From: Martin Reuter <mreu...@nmr.mgh.harvard.edu> > > Date: Wed, 30 Sep 2009 14:49:46 -0400 > > To: "Weisinger, Brian (NIH/OD) [E]" <brian.weisin...@nih.gov> > > Cc: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] How to calculate differences using the > > longitudinal data > > > > Hi Brian, > > > > after the longitudinal runs are through you have directories > > tpN.long.base for each timepoint per subject. These contain the same > > structure as the cross sectionally processed results, however the values > > (e.g. thickness, volume etc. in the stat files) should be more > > accurate. > > > > You can compare these results between timepoints in the same way you > > would do that without the longitudinal stream. You just need to take the > > more accurate information in the .long. directories instead. > > > > Best, Martin > > > > On Tue, 2009-09-29 at 14:59 -0400, Weisinger, Brian (NIH/OD) [E] wrote: > > > I have run the longitudinal stream on the scans I need, but now I am not > > > sure what to use to compare the differences. > > > If someone could clarify this for me I would really appreciate it. > > > > > > Thanks > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > ------ End of Forwarded Message > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
