Hi Laura,

the convergion threshold is very small, so it can happen that it does not reach convergion, usually that is not a problem.

You should open the norm.mgz of the base and also map the norm.mgz from each time point to the base (this is done in the -long step automatically, but you can do it manually), like that: use mri_convert -at base/mri/transforms/???.lta -rt cubic tp/mri/norm.mgz tp_to_base_norm.mgz

Then open all these images in freeview and check if the registration looks good.

I have the suspicion that something else went wrong.

Martin

On 04/11/2014 10:32 AM, L. Koenders wrote:

Dear FreeSurfer people,

I posted this question before, but I am a bit further as to where the problem lies. I have a question regarding the longitudinal pipeline. In FS v5.3.0, I ran all scans through the Cross pipeline, and made brainmask.mgz pial edits where necessary. So far so good. Subsequently, I ran all the scans (all the edited scans) through the Base pipeline. However, something is going wrong with the creation of the templates. We went through the logs, and found the following error in the logs of the failed scans:

====================== TP 2 to TP 1 ============================== Register TP 2 ( /data/home/shahand/test/104/104_FU/mri/norm.mgz ) to TP 1 ( /data/home/shahand/test/104/104_BL/mri/norm.mgz )

• WARNING: TP 2 to 1 did not converge !! computing coord of TP 2 ( /data/home/shahand/test/104/104_FU/mri/norm.mgz ) wrt to TP 1 ( /data/home/shahand/test/104/104_BL/mri/norm.mgz ) computing mean coord of TP 1 ( /data/home/shahand/test/104/104_BL/mri/norm.mgz ) mapping back to rot, err = 2.86707e-08 computing mean coord of TP 2 ( /data/home/shahand/test/104/104_FU/mri/norm.mgz ) mapping back to rot, err = 2.86707e-08

mapping movs and creating initial template... using median Writing final template: /data/home/shahand/long/104/104_template/mri/norm_template.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 registration took 4 minutes and 7 seconds

I tried to find some more information on this warning in the FreeSurfer Mailinglist archives, but did not find anything useful. Can you tell me WHY this convergence didn't take place and more importantly - how to fix it??

Looking forward to hearing your thoughts on this. Have a good weekend!

Best regards, Laura Koenders ________________________________

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