Dear Paola,
I think the problem might be that your operating system ships libtiff.so.4 instead of libtiff.so.3 and that is why mris_volmask.bin cannot find libtiff.so.3.
As far as I know you can just create a symbolic link from libtiff.so.3 to libtiff.so.4. In case your libraries are in /usr/lib usually that would be the following command in the terminal:
ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3
Maybe also have a look here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-March/007370.html http://linux.derkeiler.com/Mailing-Lists/Ubuntu/2006-04/msg02866.html
Best regards, Christian Scheel
--- University of Cologne Department of Psychiatry
Am 28.09.2010 09:40, schrieb Paola Valsasina:
Dear FS list,
I am trying to finish my first analyses with freesurfer; however, I have some problems when running the last stages of recon-all.
In summary what I did:
recon-all –autorecon1 (worked well)
some minor brain strip editing
recon-all –autorecon2 (worked well)
some editing both of white matter and adding some control points
Now I have run recon-all –autorecon2-cp –autorecon3, but I receive
the following error (after many hours of post-processing):
mris_volmask –label_left_white 2 –label_left_ribbon 3 –label_right_white 41 –label_right_ribbon 42 –save_ribbon –save_distance “subject_name”
mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory
recon-all exited with errors
Apparently, cortical segmentation has been performed, since I see in the stats folder both ?h.aparc.stats and ?h.aparc.a2009s.stats files. Which additional output am I missing because of this error?
Thank you for your help
Paola
Paola Valsasina
Research Fellow to Prof. M. Filippi
Neuroimaging Research Unit
Institute of Experimental Neurology
Hospital San Raffaele
via Olgettina 60
20132 Milan - ITALY
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