Hi Esha,

this is not how you setup a freesurfer call. What you did is create a single subjects with 1000 scans and the motion correction step tries to average all these scans into a single file. Instead you need to create for each subject a directory and put the corresponding file there:
001/mri/orig/001.mgz
002/mri/orig/001.mgz (you call it again 001 but it is a different image than the one from the first subject)
003/mri/orig/001.mgz
…

then you run recon-all a thousand times like
recon-all -autorecon1 -autorecon2 -subjid 001
recon-all -autorecon1 -autorecon2 -subjid 002
…

you can also do recon-all -all -subjid 001 (if you want to include the surface stuff). 

The directory that contains all the 001, 002 .. directories is called the SUBJECTS_DIR and needs to be specified (either as environment variable or on  the command line with the -sd flag to tell recon-all where to find the individual directories for each subject.

Best, Martin

On Aug 6, 2014, at 10:37 PM, Esha Mehta <emehta15@gwmail.gwu.edu> wrote:

Hi Bruce, 

The exact command I ran was  recon-all -autorecon1 -autorecon2 -subjid DNS_highRes_N892

I do have ~1000 scans, but it is not a longitudinal study. They are located under the DNS_highRes_n892/mri/orig/ directory in the .mgz format. 

Let me know if you need anymore information. Thanks!


On Wed, Aug 6, 2014 at 3:09 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Esha

what are you trying to do? From this output it looks like you are runing a ~1000 time point longiutdinal study, which I assume is not what you meant.

Please be sure to include the exact command you ran!

cheers
Bruce


On Wed, 6 Aug 2014, Esha Mehta wrote:

Hello, 
I am extremely new FreeSurfer user, and have hit a bump in the road while
trying to run -autorecon1 and -autorecon2. The process seemed to be running
smoothly until I got the following warning messages for every file number,
and then it was randomly killed- 

* WARNING: TP 890 to 1 did not converge !! 

* WARNING: TP 891 to 1 did not converge !! 

* WARNING: TP 892 to 1 did not converge !! 

mapping movs and creating initial template...

 allow intensity scaling

Linux login4 2.6.32-431.5.1.el6.x86_64 #1 SMP Fri Jan 10 14:46:43 EST 2014
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s DNS_highRes_N892 exited with ERRORS at Mon Jul 21 10:48:23 EDT
2014


Within the error log, there was also an extremely lengthy command, and I
believe could have been part of the issue as well. It is way to long to post
here, but here is how it begins and ends-

CMD mri_robust_template --mov
/groups/wallacegrp/DNS_highRes_N892/mri/orig/000.mgz
/groups/wallacegrp/DNS_highRes_N892/mri/orig/001.mgz
/groups/wallacegrp/DNS_highRes_N892/mri/orig/002.mgz

...

/groups/wallacegrp/DNS_highRes_N892/mri/orig/888.lta
/groups/wallacegrp/DNS_highRes_N892/mri/orig/889.lta
/groups/wallacegrp/DNS_highRes_N892/mri/orig/890.lta
/groups/wallacegrp/DNS_highRes_N892/mri/orig/891.lta


I was hoping you could give me some advice on how to deal with this error,
or help me determine whether this is a freesurfer error, or has to do with
something else.

Thanks so much!

--
Esha Mehta585-967-7223
emehta15@gwu.edu
George Washington University, Class of 2017


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--
Esha Mehta
585-967-7223
emehta15@gwu.edu
George Washington University, Class of 2017
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---------------------------------
Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: