Freesurfer October 2005

freesurfer@nmr.mgh.harvard.edu

49 participants
62 discussions

make_average_subject error?
by Brian Schweinsburg, Ph.D. 02 Oct '05

02 Oct '05

Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything. make_average_subject --subjects SC010 SC011 SC012 ... I am running the latested dev release with Fedora Core 4. Any ideas as to the problem? Brian

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recon-all error
by Morgan Hough 02 Oct '05

02 Oct '05

I downloaded the latest freesurfer-dev and I was testing out my install with "recon-all -autorecon-all -subjid bert" and I am getting this error. mri_convert nu4.mnc nu.mgz mincRead(): can't find file /var/scratch11/mhough/subjects/bert/mri/nu4.mnc reading from nu4.mnc... ERROR: converting nu to COR/mgz The file certainly isn't there and I don't see anything in mri/norm if that is where it should be. Here's what there is: [mhough@dhania bert]$ find . -name "*.mnc" ./mri/tmp-mri_motion_correct2-32472/cor-1.mnc ./mri/tmp-mri_motion_correct2-32472/cor-2.mnc ./mri/tmp-mri_motion_correct2-32472/cor-3.mnc [mhough@dhania bert]$ which nu_correct /usr/local/freesurfer/lib/mni/bin/nu_correct Just to double check it wasn't something special about bert I created a new directory for my one subject that I want to process and I got the same error. Thanks in advance. Cheers, -Morgan -- Morgan G. Hough, DPhil Candidate University of Oxford, Centre for Functional MRI of the Brain (FMRIB) John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom Tel: +44 (0) 1865 222545 / Fax: +44 (0) 1865 222717 e-mail: mhough(a)fmrib.ox.ac.uk / URL: http://www.fmrib.ox.ac.uk/~mhough

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Freesurfer October 2005