[Freesurfer] mnc2nii input file problem

2011-01-25 Thread Alexander Zaitsev
Hello: When I am trying to convert mnc file into nifti, the mnc2nii converter gives me an error $FREESURFER_HOME/mni/bin/mnc2nii fileName.mnc fileName.nii "Can't find input file fileName.mnc" Prepending a whole path to the file name does not help - same error message I am using FreeSurver 5.0.0

Re: [Freesurfer] processing time for autorecon1 in Freesurfer v4.5

2009-10-17 Thread Alexander Zaitsev (CNI)
the steps taking longer, or are some binaries longer than others > > On Thu, 15 Oct 2009, Alexander Zaitsev > (CNI) wrote: > > >> We are having the same issue after upgrade to FreeSurfer 4.5. >> It takes more than 1.5 hrs for the jobs that used to complete in less

Re: [Freesurfer] processing time for autorecon1 in Freesurfer v4.5

2009-10-15 Thread Alexander Zaitsev (CNI)
We are having the same issue after upgrade to FreeSurfer 4.5. It takes more than 1.5 hrs for the jobs that used to complete in less than 30 minutes. Alex Zaitsev Chris Hyatt wrote: > > We recently installed a Dell Blade server cluster running Freesurfer > v4.5 under CentOS 64-bit Linux, with e

Re: [Freesurfer] mri_convert for DICOM PD_T2 images

2009-08-27 Thread Alexander Zaitsev
Please disregard my request: Have to use -f 0 -f 1 for frame selection (mri_convert -- help looks vague for -f flag Thank you, Alex Alexander Zaitsev wrote: > Hello: > > I have DICOM PD/T2 dual echo images. > Is it possible to generate two NIFTI files PD.nii and T2.nii using &

[Freesurfer] mri_convert for DICOM PD_T2 images

2009-08-27 Thread Alexander Zaitsev
Hello: I have DICOM PD/T2 dual echo images. Is it possible to generate two NIFTI files PD.nii and T2.nii using mri_convert? Thank you, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f

[Freesurfer] Calling mri_convert from Java code

2008-02-25 Thread Alexander Zaitsev (CNI)
Hello: I need to call mri_convert utility from Java code. The problem is when I am making a system call, I am getting the following error : > FreeSurfer license file /Application/freesurfer/.license not found. If you are outside the NMR-Martinos center, go to http://surfer.nmr.mgh.harvard