Petr why do you keep trying to name your input files something.mgz, when you were in wisconsin i told you the inputs always need to be 001.mgz
at this point i think you need to get invited to upload one of your data sets to ugh and see if there is a problem with the data or is it a problem with your computer. Can someone there at martinos invite Petr to upload the dataset and tell him the mechanism for doing this ? On 01/18/13, zach.p...@post.cz wrote: > > > > > I tried on another standar PC (4 core processor) with XP Win recon-all in > VirtualBox (latest edition) running Ubuntu. > > > > I attach file folder with patient brain - first in VirtualBox as described > and then in command line of terminal Ubuntu window: > > sudo mount - vboxsf folder /home/virtualuser/freesurfer/subjects/folder > > > > Then I convert original TrioTim scanner files using mri_convert -it IMA -ot > mgz filename foldername.mgz > > * here is slight problem - recon log shows that mri_convert recognizes itself > that although my brain files are labeled as IMA that they are not old Siemens > files, so that it unpacks them as DICOM and suggests that if it fails I > should run mri_convert as DICOM > > But after all mri_convert succesfully writes foldername.mgz file as a result > of conversion in foldername directory > > > > Ok, then I run recon-all -subjid foldername -autorecon1 -cw256 > > Now -cw256 was suggested in another error run because files do not fit in 256 > matrix > > Recon stops and sayz no 001.mgz files in /mri/orig directory > > So I copy converted foldername.mgz from foldername directory into /mri/orig > directory and rename it to 001.mgz > > *now here is my question: do all people get 001.mgz file the same way as me? > > Then when I run recon-all -subjid foldername -autorecon1 -cw256 it halts with > error at nu_correct as you can see in attached recon-all.log file > > > > Petr _______________________________________________ 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.
