Hi Stefano,

If you suspect that the error is due to the small deformation values, can you try to use -odt float to specify the output data format?

Lilla

On Tue, 29 Oct 2019, Stefano Zappala wrote:

Hi there,

I am having problem reading the final_CVSmorph_toS131032017_Supine.m3z transform as output of the mri_cvs_register function. I used mri_convert final_CVSmorph_toS131032017_Supine.m3z final_CVSmorph_toS131032017_Supine.nii.gz to convert the transform file to nifti format but what I get it's just a map of zeros.

I have checked any different source of error:

• mri_convert: it works because if I convert /transforms/talairach.m3z to nifti the conversion is successful;
• mri_cvs_register: it works because the two images are aligned very well and correspond perfectly;
• final_CVSmorph_toS131032017_Supine: it is not empty because if I run mri_convert -at final_CVSmorph_toS131032017_Supine.m3z firstScan/mri/T1.mgz secondScan/mri/T1mine.mgz  the result is morphed correctly. So the transform final_CVSmorph_toS131032017_Supine is actually not populated with zeros.

So it could be a problem of type of data: the transform should be indeed populated with very small values, since the difference between the scans even if noticeable, it is very small.

I don't know what to try anymore: I was wondering if you have any suggestion? In summary, the call to mri_cvs_register is successful giving me as output a transform in .m3z format which is not zero. When I try to convert it to nifti file, the transformation results full of zeros.

1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2. Platform: Ubuntu 18.04.3 LTS
3. uname -a: Linux zappst-Q170M-C 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/LinuxThu Aug 13 22:55:16 UTC

2015 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log for only one of the two images registered: see attached 5) mri_cvs_register.log: see attached

Many thanks, Stefano.

Stefano Zappalá                                                      Stefano Zappalá PhD Student                                                             Myfyrwraig PhD School of Computer Science & Informatics        Yr Ysgol Cyfrifiadureg a Gwybodeg Cardiff University                                                     Prifysgol Caerdydd 5 The Parade                                                            5 The Parade Cardiff                                                                       Caerdydd CF24 3AA                                                                  CF24 3AA Tel: +44 (0)7943096049                                         Ffôn: +44 (0)7943096049