This is a known issue with the VirtualBox installation of freesurfer and is related to the mni tools. The mri_nu_correct stage will fail when subjects directory is in a shared folder between the host machine and the VirtualBox environment. Only known solution is to import the entire subject data into the virtual machine.
-Zeke On 02/11/2016 08:48 AM, Bruce Fischl wrote: > yes, something wrong with the installation but it's outside of my > expertise. Zeke: can you take a look? > > thanks > Bruce > On Thu, 11 Feb 2016, Zoellner, Frank wrote: > >> 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 >> >> >> _______________________________________________ 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.
