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.ukmailto:espezi@cardiff.ac.uk
Dr Daniel Gallichan Ddarlithydd
CUBRIC Ysgol Beirianneg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ Cymru, y Deyrnas Unedig
Ffôn: +44 (0) 29 208 70045 E-bost: gallichand@caerdydd.ac.ukmailto:gallichand@caerdydd.ac.uk
Personal website: http://www.cardiff.ac.uk/people/view/507850-gallichan-daniel CUBRIC - Cardiff University Brain Research Imaging Centre - http://sites.cardiff.ac.uk/cubric/
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
Ffôn: +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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