Hi Martin, Excellent, it works just fine without the --initorient. However, I'd be happy to help test the fixed version. I'm running the stable v5.3 linux distribution (actual OS is Debian 'jesse' 8.1).
Thanks, Andrew On Wed, Sep 23, 2015 at 11:12 PM <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > Hi Andrew, > > yes, something is wrong with the --initorient > you can simply drop it, it registers fine without it. There are > non-linearities in your image, so maybe you want to add --affine to get it > match better (depending on what this is and what you are using this for). > > Ha, just found the bug. OK fixed. :-). Let me know your operating system > and we can point you to the fixed version for testing. > > Still you may not need --initorient for your data. > > Best, Martin > > > On 09/23/2015 03:20 PM, Andrew Floren wrote: > > Hello all, > > I've encountered a potential bug in mri_robust_register. For a particular > pair of source and target volumes the command: > > mri_robust_register --satit --initorient --lta robustreg.lta --mov > source.mgz --dst target.mgz > > fails with the following error message: > > mri_robust_register: Registration.cpp:3301: vnl_matrix_fixed<double, 4u, > 4u> Registration::initializeTransform(MRI*, MRI*): Assertion `fcount ==0 || > fcount==2' failed. > > I am unsure as to what fcount refers to but mri_info and inspection via > freeview shows nothing out of the ordinary. I use this command as part of > my preprocessing pipeline and this is the only pair of volumes for which > the command fails. > > bugr output: > --------------------------------------------------------------------- > FREESURFER_HOME: /opt/freesurfer > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Debian version: 8.1 > Kernel info: Linux 3.16.0-4-amd64 x86_64 > --------------------------------------------------------------------- > > I've also made an archive containing the offending volumes and a short > bash script that should reproduce the error available at: > https://drive.google.com/file/d/0B-KO9yz4-k1mbHgwM3hoNEFTOWM/view?usp=sharing > > Any and all help is greatly appreciated, > Andrew > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu > >
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