Hi, did you find a hint why my installation of freesurfer is not processing the data at that stage ? It seems to be a general problem, we tried also with other data sets of elder people etc ..
Any help appreciated. Yours Frank ---------------- PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: frank.zoell...@medma.uni-heidelberg.de Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/ -----Ursprüngliche Nachricht----- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Zoellner, Frank Gesendet: Dienstag, 9. Februar 2016 15:49 An: Freesurfer support list Betreff: Re: [Freesurfer] Processing of young children using Freesurfer Hi Bruce, thanks for the reply. Here comes the output (see attached). I just downloaded the VM with freesurfer from your website, fyi. Yours Frank ---------------- PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: frank.zoell...@medma.uni-heidelberg.de Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/ -----Ursprüngliche Nachricht----- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 9. Februar 2016 14:12 An: Freesurfer support list Betreff: Re: [Freesurfer] Processing of young children using Freesurfer hmmm, this doesn't seem to have to do with your data but maybe is an installation problem? It says it failed but doesn't give an error message, which is unusual. Can you try just typing in directly: cd /media/sf_cdh_ventrikel/test_002/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz and send us the output? cheers Bruce On Tue, 9 Feb 2016, Zoellner, Frank wrote: > Hi, > > I am currently working on a project involving brain morphometry of 2 > year old children. > We are interested in segmenting the ventricle and I tried to run > freesurfer using the standard recon-all -all for a first test. > > Unfortunately, freesurfer reports an error (see attached log file). > > I also read about that it is advised to run freesurfer with patient > age >5 but maybe someone has an idea how to solve this. > As far as I get from the step it crashes at the intensity correction step? > Do I need to calculate some sort of template maybe ? > > Any comments welcome > > Yours > Frank > > ---------------- > PD Dr. Frank Zoellner > Group Leader "MRI and Medical Image Analysis" > Computer Assisted Clinical Medicine > Medical Faculty Mannheim > Heidelberg University > Theodor-Kutzer-Ufer 1-3 > D-68167 Mannheim > > Phone: +49 (0)621 3835117 > Fax: +49 (0)621 3835123 > Email: frank.zoell...@medma.uni-heidelberg.de > Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/ > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
