That appears to work perfectly, thanks!
I’m confused, though, as to me the direction of the operations appears to be reversed (the reg.dat file was obtained by moving the hires MRI to match the low-res surface). How do I know which one to use?
On 14 Jun 2017, at 17:00, freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu wrote:
Date: Wed, 14 Jun 2017 16:56:17 +0200 From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Applying an affine transformation to a surface To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <ba337251-ab46-8ef2-a1f3-25dbbd353776@nmr.mgh.harvard.edumailto: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.ukmailto: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.ukmailto: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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