Dear Lilla,

thank you for your prompt response.

I have just applied mri_vol2vol, calling for

mri_vol2vol --mov $folder/w_MniNick.nii --targ $folder/MniNick.nii - --o $folder/outvol.mgz --m3z $folder/final_CVSmorph_toSynthF.m3z --noDefM3zPath --no-save-reg.

Unfortunately, the result is not what I was expecting, as the deformation is not anatomically acceptable in certain regions.

Therefore, I was wondering how to view the warp field in order to check whether the mri_cvs_register or the mri_vol2vol call fails. I couldn't find any information on how to do it on the FS website.

Thank you very much for your consideration.

Best, Stefano. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: 11 January 2017 18:56:07 To: Freesurfer support list Subject: Re: [Freesurfer] createMorph & applyMorph: unexpected results

Hi Stefano,

If you have the final_CVSmorph_toSynthF.m3z file you can use mri_vol2vol dirctly to apply it to another volume. Look for examples in mri_cvs_register --help.

We are moving away from using the tm3d file format.

Lilla

On Wed, 11 Jan 2017, Stefano Zappalà wrote:

Hello FreeSurfer Developers,

I'm attempting to apply the CVS output transformation "final_CVSmorph_toSynthF.m3z" to an image different to the one that was used for its estimation. I followed the steps reported at the bottom of the page https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register, adjusting the lines for the output files that I obtained from mri_cvs_register. So I called for

mri_cvs_register - Free Surfer Wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register surfer.nmr.mgh.harvard.edu Name. mri_cvs_register - registers MRI scans of two subjects (or a subject and the CVS atlas) using the combined volume and surface-based registration method, CVS.

  createMorph --out fullCVSmorph.tm3d --template MniNick.mgz --subject w_MniNick.mgz --in gcam final_CVSmorph_toSynthF.m3z morph el_reg_toSynthF.mgz

and applyMorph --template MniNick.mgz --transform fullCVSmorph.tm3d vol w_MniNick.mgz outputvol.nii trilinear

but I encountered the following output when running createMorph:

setting orig areas to linear transform determinant scaled 1.00 atlas geometry = 256 , 256 , 256 image geometry = 256 , 256 , 256 vox 2 ras atlas = -1.00000 0.00000 0.00000 127.00000; 0.00000 0.00000 1.00000 -145.00000; 0.00000 -1.00000 0.00000 147.00000; 0.00000 0.00000 0.00000 1.00000; ras 2 vox image = -1.00000 -0.00000 -0.00000 90.00000; -0.00000 1.00000 -0.00000 126.00000; -0.00000 -0.00000 1.00000 72.00000; -0.00000 -0.00000 -0.00000 1.00000; product = 1.00000 0.00000 0.00000 -37.00000; 0.00000 0.00000 1.00000 -19.00000; 0.00000 -1.00000 0.00000 219.00000; 0.00000 0.00000 0.00000 1.00000;

transform at origin -37.00000; -19.00000; 219.00000; 1.00000; invalid voxel count = 0 extension = mgz terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped)

I've searched the mailing list and no similar errors have been reported. The recon-all and mri_cvs_register calls seemed to have correctly terminated. Does anyone have any thoughts on how to trouble-shoot this one?

1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-dev-20161130-24fa2c9
2. Platform: ubuntu 16.04 LTS
3. In the attachment:

3.1) log files of the mri_cvs_register execution; 3.2) log file of the recon-all executions on the moving and fixed images.

Thank you for your consideration.

Stefano.