Dear Freesurfer user
I posted this question already on the mailing list and understood the answer. But this failure only occures when running on the grid. When I run the Freesurfer locally with the same brains, the error did not occur. Unfortunately, I have Fs version 3.0.4 on the grid and 3.0.3 on my local machine.
What other kind of problem could also produce that error message?
When I looked in the directory of these subjects, only 3 folders are present (mri, scripts, touch) instead 10 as normal. I got the impression that not all environmental variables are set properly.
Could it be that the missing folders caused the problem?
Thanks in advance Best regards Juergen
Hi Juergen,
yes, this usually means the talairach is bad. Either run without it or fix it manually I guess. Bruce On Tue, 19 Dec 2006, Juergen Haenggi, Psychiatrische Uni-Klinik wrote:
Dear Freesurfer users
While running recon-all, the following error occured:
#-------------------------------------------- #@# Intensity Normalization Sat Dec 16 13:10:39 CET 2006 /scratch/bli/AN1792/subjects/Patient02_2002/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.796 -0.256 -0.057 -8195.100; 0.086 0.398 -0.583 12578.642; 0.224 0.596 0.440 21656.441; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux node0214 2.6.15.6-id-x86_64-k8-smp #1 SMP Wed Mar 22 12:35:20 CET 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Dec 16 13:10:41 CET 2006
If I try to check the talairach.xfm with tkregister2, I see only a little part of the brain in the left upper corner of the graphic window. Because the DICOM files used
were converted from ANALYSE files, I guess that there is a problem with the coordinate origin of the DICOMs.
Could it be that this is the cause of my problem?
The transformation matrix seems also not OK.
Because I have about 250 brains which is the fastest way to
fix that problem?
Thanks in advance
Best regards
Juergen
Juergen Haenggi, Ph.D. student Psychiatric University Hospital Division of Psychiatry Research University of Zurich, Switzerland PO Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi@bli.unizh.ch (division email)
(division website) http://www.juergenhaenggi.ch (private website)
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Juergen Haenggi