On 14 Jun 2017, at 17:00, freesurfer-request@nmr.mgh.harvard.edu wrote:

Date: Wed, 14 Jun 2017 16:56:17 +0200
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Applying an affine transformation to a
surface
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <ba337251-ab46-8ef2-a1f3-25dbbd353776@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Can you try it with --reg instead of --reg-inv ?

On 6/13/17 8:55 PM, Daniel Gallichan wrote:

Hello

In a very similar situation to a post I found in the Freesurfer
archive, I have low-resolution (3T) and high-resolution scans (7T) of
the same subject - and would like to put the surfaces from the
low-resolution scan into the space of the hi-res data. The
instructions from the previous thread say to check example 4 when
running ?mri_surf2surf --help? - which I tried, but I cannot get the
result to overlap in freeview.

I have a registration file which looks very good from running
bbregister on the high-res data into the low-res space - but I cannot
perform the registration the other way around as I?m still having
trouble getting the hi-res data to process properly through recon-all
(it?s acquired at 350um, and I?m currently running it downsampled to
500um, but that?s still a work-in-progress?).

So this is the command-line that I tried to apply the transformation
from the registration to a surface:

mri_surf2surf --reg-inv hires_to_lowres.dat
${SUBJECTS_DIR}/subj_hires/mri/T1.mgz --hemi lh --sval-xyz white
--tval-xyz ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz --tval lh.white.hires
--s subj_lowres

If I then try to view the result:

freeview -v ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz -f
${SUBJECTS_DIR}/subj_lowres/surf/lh.white.hires

it is clear that the two are far from being aligned?

I?m afraid I may be misunderstanding how to control the coordinate
systems in the mri_surf2surf command - especially as the source and
targets are different ?subjects? (the same actual subject, though?). I
can?t used the ?--trgsubject? option because recon-all has not
completed properly on the hires data, and there is no sphere.reg file
(although I have to confess, I haven?t understood why it would need it
if I am specifying my own registration file?) . Any suggestions very
gratefully received.

Thanks

Daniel

*Dr Daniel Gallichan*
*Lecturer*

CUBRIC
School of Engineering
Cardiff University
Maindy Road
Cardiff
CF24 4HQ
Wales, United Kingdom

Tel: +44 (0) 29 208 70045
Email: gallichand@cardiff.ac.uk <mailto:gallichand@cardiff.ac.uk>

*Dr Daniel Gallichan*
*Ddarlithydd*

CUBRIC
Ysgol Beirianneg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
Cymru, y Deyrnas Unedig

Ff?n: +44 (0) 29 208 70045
E-bost: gallichand@caerdydd.ac.uk <mailto:gallichand@caerdydd.ac.uk>

Personal website:
http://www.cardiff.ac.uk/people/view/507850-gallichan-daniel
CUBRIC - *C*ardiff *U*niversity *B*rain *R*esearch *I*maging
*C*entre - http://sites.cardiff.ac.uk/cubric/

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