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" mreuter@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.Weisinger@nih.gov Date: Thu, 1 Oct 2009 14:26:23 -0400 To: Nitin Gogtay gogtayn@mail.nih.gov Subject: FW: [Freesurfer] How to calculate differences using the longitudinal data
------ Forwarded Message From: Martin Reuter mreuter@nmr.mgh.harvard.edu Date: Wed, 30 Sep 2009 14:49:46 -0400 To: "Weisinger, Brian (NIH/OD) [E]" Brian.Weisinger@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
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------ End of Forwarded Message