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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--------------------------------- 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: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu