Freesurfer January 2007

freesurfer@nmr.mgh.harvard.edu

51 participants
74 discussions

recon-all -autorecon2-cp
by Shi, Bo 03 Jan '07

03 Jan '07

Does recon-all -autorecon2-cp ... Remove all previous manual white-matter edits? Is there a way I can prevent this? -- Bo Shi 300 Longwood Ave Pavilion 152 Boston, MA 02115 (617) 355-5167

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WG: [Freesurfer] MRInormalize: could not find any valid peaks
by Juergen Haenggi 03 Jan '07

03 Jan '07

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(a)bli.unizh.ch (division email) > http://www.dpr.unizh.ch/ > > (division website) http://www.juergenhaenggi.ch (private website) > > ----------------------------------------------- > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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talairach questions
by Dominick, Kelli, Ray Carpenter 02 Jan '07

02 Jan '07

Hi All, We have had a number of brains with very bad talairach transforms however aparc+aseg looks fine. In addition, while the talairach.xfm transform is very bad talairach.Ita is not. Is the bad xfm transform still a problem even though it is not affecting the labels. And if so which transform should I attempt to correct in tkregister2 in order to fix the problem? (I ask because it looks like that some of the tutorials still refer to old file names that have changed in the stable versions). I am using v3.03. Thanks in advance for your help! Kelli

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DICOM format
by Kaoru Amano 02 Jan '07

02 Jan '07

Though I need Dicom data, files in the MGH format (.bshort, .bfloat) are currently available. "mri_convert" seems to accept dicom format only as an input. Is there a way to get Dicom data from MGH data? Regrds, Kaoru Amano

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Freesurfer January 2007