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: > > > > > > #-------------------------------------------- > > [EMAIL PROTECTED] 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) > > [EMAIL PROTECTED] (division email) > http://www.dpr.unizh.ch/ > > (division website) http://www.juergenhaenggi.ch (private website) > > ----------------------------------------------- > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
