Not sure about mris_transform, but you can use
mris_applyreg --lta source-surf ltafile output-surf
You will have to convert your flirt reg to lta (lta_convert --infsl
flirt.mtx --outlta flirt.lta --src flirtinput.nii --trg flirtoutput.nii)
On 10/13/2022 9:40 PM, Chris Adamson wrote:
External Email - Use Caution
Freesurfer experts,
I’m trying to put some subject surfaces into a template space. I have
performed the following flirt registration per subject:
flirt -in $SUBJECTS_DIR/$CURSUBJECT/mri/T2.nii.gz -ref
template0.nii.gz -omat
$SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.fslmat -out
$SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.nii.gz -dof 12
-searchrx -$D $D -searchry -$D $D -searchrz -$D $D
Then apply the flirt transform
mris_transform --trx-src $SUBJECTS_DIR/$CURSUBJECT/mri/T2.nii.gz
--trx-dst template0.nii.gz
$SUBJECTS_DIR/$CURSUBJECT/surf/${CURHEMI}.${CURSURFTYPE}
$SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.fslmat
$SUBJECTS_DIR/$CURSUBJECT/surf/${CURHEMI}.${CURSURFTYPE}.flirt
When I overlay the output surface
$SUBJECTS_DIR/$CURSUBJECT/surf/${CURHEMI}.${CURSURFTYPE}.flirt over
the template template0.nii.gz the surface is in the wrong orientation
and in the wrong position, i.e. not correct.
I have tried using lta_convert to make a lta transform and I get the
same result.
Any thoughts?
Thanks,
Chris.
*Dr Chris Adamson*
Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3
EFT)
Software Engineer, Cardiovascular Research (0.7 EFT)
*Murdoch Childrens Research Institute*
The Royal Children’s Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adam...@mcri.edu.au <mailto:chris.adam...@mcri.edu.au>
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