Hi Siddharth,

if you plan to run the full longitudinal stream in 3), you need the aseg.mgz files in each cross sectional directory. so 3 should not complete unless the aseg.mgz is available in all timepoints in the cross sectional runs (1). In fact we recommend to run the full recon-all -all on each time point independently in 1), even though the surfaces are currently not used in the template and long runs, it does not hurt to have them available for the future.

I'd recommend to rerun everything from scratch to analyze where things fail, use -all for the three steps 1) cross, 2) base and 3) long.

If you still run into problems, please post the exact commands you issued and the FreeSurfer version you use.

Good luck Martin

On 09/09/2013 10:32 AM, Ray, Siddharth wrote:

Hi all,

I was trying to run freesurfer longitudinal analysis for my subjects at 2 time points and when I ran the pre_proc step it gave me an error that file ‘lh/rh.thickness is missing’. Here is what I have done.

1)      Run the Freesurfer till CA Normalize stage (till norm.mgz stage).

2)      Created unbiased template – log file showed ‘exited without error’ (and it looks fine)

3)      Run longitudinal processing – log file showed ‘exited without error’ , but when I closely looked at the file there was following error:

#@# Talairach Failure Detection Wed Sep 4 14:22:01 CDT 2013

/work/02510/sray2/Free_Sub/FS_output/54062.long.54062_59467/mri

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0124, pval=0.0000 < threshold=0.0050)

Do you where is I am doing wrong. Why is the log file showing ‘exited without error’ if there was an error at Talairach Detection.

Please let me know.

Thanks,

-Siddharth
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Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

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