Ok thx for the info. Yours Frank
> Am 11.02.2016 um 17:29 schrieb Z K <zkauf...@nmr.mgh.harvard.edu>: > > 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 >>> >>> >>> > > > 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. > ---------------- 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
